chrX-53394801-C-T

Variant names:

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2

The NM_006306.4(SMC1A):c.2950G>A(p.Gly984Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000846 in 1,182,200 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.0000096 ( 0 hom., 0 hem., cov: 20)

Exomes 𝑓: 0.0000083 ( 0 hom. 1 hem. )

Consequence

SMC1A
NM_006306.4 missense

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:2

Conservation

PhyloP100: 5.30

Publications

0 publications found

Variant links:

Genes affected

SMC1A (HGNC:11111): (structural maintenance of chromosomes 1A) Proper cohesion of sister chromatids is a prerequisite for the correct segregation of chromosomes during cell division. The cohesin multiprotein complex is required for sister chromatid cohesion. This complex is composed partly of two structural maintenance of chromosomes (SMC) proteins, SMC3 and either SMC1B or the protein encoded by this gene. Most of the cohesin complexes dissociate from the chromosomes before mitosis, although those complexes at the kinetochore remain. Therefore, the encoded protein is thought to be an important part of functional kinetochores. In addition, this protein interacts with BRCA1 and is phosphorylated by ATM, indicating a potential role for this protein in DNA repair. This gene, which belongs to the SMC gene family, is located in an area of the X-chromosome that escapes X inactivation. Mutations in this gene result in Cornelia de Lange syndrome. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2013]

SMC1A Gene-Disease associations (from GenCC):

Cornelia de Lange syndrome 2
Inheritance: XL Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
developmental and epileptic encephalopathy, 85, with or without midline brain defects
Inheritance: XL Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
X-linked complex neurodevelopmental disorder
Inheritance: XL Classification: DEFINITIVE Submitted by: ClinGen
atypical Rett syndrome
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Cornelia de Lange syndrome
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

SMC1A links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -9 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.057444155).

BP6

Variant X-53394801-C-T is Benign according to our data. Variant chrX-53394801-C-T is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 463884.

BS2

High AC in GnomAdExome4 at 9 AD,XL gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006306.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMC1A	NM_006306.4	MANE Select	c.2950G>A	p.Gly984Ser	missense	Exon 19 of 25	NP_006297.2
	SMC1A	NM_001281463.1		c.2884G>A	p.Gly962Ser	missense	Exon 20 of 26	NP_001268392.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
SMC1A	ENST00000322213.9	TSL:1 MANE Select	c.2950G>A	p.Gly984Ser	missense	Exon 19 of 25	ENSP00000323421.3
SMC1A	ENST00000375340.10	TSL:1	c.2884G>A	p.Gly962Ser	missense	Exon 20 of 26	ENSP00000364489.7
SMC1A	ENST00000675504.1		c.2884G>A	p.Gly962Ser	missense	Exon 19 of 25	ENSP00000502524.1

Frequencies

GnomAD3 genomes

AF:

0.00000962

AC:

AN:

103938

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000354

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.0000219

AC:

AN:

182884

AF XY:

0.00

show subpopulations

Gnomad AFR exome

AF:

0.0000760

Gnomad AMR exome

AF:

0.0000729

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000835

AC:

AN:

1078262

Hom.:

Cov.:

AF XY:

0.00000289

AC XY:

AN XY:

346246

show subpopulations

African (AFR)

AF:

0.0000384

AC:

AN:

26019

American (AMR)

AF:

0.0000854

AC:

AN:

35111

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

19168

East Asian (EAS)

AF:

0.00

AC:

AN:

30014

South Asian (SAS)

AF:

0.0000186

AC:

AN:

53722

European-Finnish (FIN)

AF:

0.00

AC:

AN:

40009

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4075

European-Non Finnish (NFE)

AF:

0.00000364

AC:

AN:

824787

Other (OTH)

AF:

0.0000220

AC:

AN:

45357

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.431

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00000962

AC:

AN:

103938

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

26742

show subpopulations

African (AFR)

AF:

0.0000354

AC:

AN:

28213

American (AMR)

AF:

0.00

AC:

AN:

9600

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2535

East Asian (EAS)

AF:

0.00

AC:

AN:

3269

South Asian (SAS)

AF:

0.00

AC:

AN:

2097

European-Finnish (FIN)

AF:

0.00

AC:

AN:

5406

Middle Eastern (MID)

AF:

0.00

AC:

AN:

233

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

50577

Other (OTH)

AF:

0.00

AC:

AN:

1361

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.575

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.0000151

ExAC

AF:

0.0000494

AC:

ClinVar

ClinVar submissions as Germline

Significance:Conflicting classifications of pathogenicity

Revision:criteria provided, conflicting classifications

View on ClinVar

Pathogenic

VUS

Benign

Condition

Congenital muscular hypertrophy-cerebral syndrome (1)

Inborn genetic diseases (1)

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.064

BayesDel_addAF

Benign

-0.41

BayesDel_noAF

Benign

-0.63

CADD

Benign

(source)

DANN

Benign

0.29

DEOGEN2

Benign

0.15

FATHMM_MKL

Benign

0.51

LIST_S2

Benign

0.83

M_CAP

Uncertain

0.22

MetaRNN

Benign

0.057

MetaSVM

Benign

-0.93

MutationAssessor

Benign

-2.4

PhyloP100

5.3

PrimateAI

Uncertain

0.51

PROVEAN

Benign

2.3

REVEL

Benign

0.23

Sift

Benign

1.0

Sift4G

Benign

1.0

Polyphen

0.0

Vest4

0.034

MutPred

0.28

Loss of catalytic residue at G984 (P = 0.0473)

MVP

0.51

MPC

1.5

ClinPred

0.064

GERP RS

3.0

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.11

gMVP

0.13

Mutation Taster

=89/11

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over