chrX-53383250-C-A

Position:

chrX-53383250-C-A

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 3P and 12B. PM1PP2BP4_ModerateBP6_ModerateBS1BS2

The NM_006306.4(SMC1A):c.2977G>T(p.Ala993Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000128 in 1,167,538 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 46 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. A993A) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.000054 ( 0 hom., 0 hem., cov: 22)

Exomes 𝑓: 0.00014 ( 0 hom. 46 hem. )

Consequence

SMC1A
NM_006306.4 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.56

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

PM1

In a coiled_coil_region (size 77) in uniprot entity SMC1A_HUMAN there are 8 pathogenic changes around while only 2 benign (80%) in NM_006306.4

PP2

Missense variant in gene, where missense usually causes diseases (based on misZ statistic), SMC1A. . Gene score misZ 6.4479 (greater than the threshold 3.09). GenCC has associacion of gene with Cornelia de Lange syndrome, X-linked complex neurodevelopmental disorder, atypical Rett syndrome, Cornelia de Lange syndrome 2, developmental and epileptic encephalopathy, 85, with or without midline brain defects.

BP4

Computational evidence support a benign effect (MetaRNN=0.1260258).

BP6

Variant X-53383250-C-A is Benign according to our data. Variant chrX-53383250-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 569413.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4_exome allele frequency = 0.000135 (143/1056342) while in subpopulation NFE AF= 0.000171 (140/820621). AF 95% confidence interval is 0.000147. There are 0 homozygotes in gnomad4_exome. There are 46 alleles in male gnomad4_exome subpopulation. Median coverage is 30. This position pass quality control queck.

BS2

High Hemizygotes in GnomAdExome4 at 46 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SMC1A	NM_006306.4 linkuse as main transcript	c.2977G>T	p.Ala993Ser	missense_variant	20/25	ENST00000322213.9
SMC1A	NM_001281463.1 linkuse as main transcript	c.2911G>T	p.Ala971Ser	missense_variant	21/26

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SMC1A	ENST00000322213.9 linkuse as main transcript	c.2977G>T	p.Ala993Ser	missense_variant	20/25	1	NM_006306.4	P1

Frequencies

GnomAD3 genomes

AF:

0.0000540

AC:

AN:

111196

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

33388

show subpopulations

Gnomad AFR

AF:

0.00

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:

0.0000944

Gnomad OTH

AF:

0.000671

GnomAD3 exomes

AF:

0.0000252

AC:

AN:

119266

Hom.:

AF XY:

0.0000247

AC XY:

AN XY:

40466

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000641

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.000135

AC:

143

AN:

1056342

Hom.:

Cov.:

AF XY:

0.000134

AC XY:

AN XY:

344146

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000171

Gnomad4 OTH exome

AF:

0.0000675

GnomAD4 genome

AF:

0.0000540

AC:

AN:

111196

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

33388

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000944

Gnomad4 OTH

AF:

0.000671

Bravo

AF:

0.0000302

ExAC

AF:

0.0000293

AC:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Congenital muscular hypertrophy-cerebral syndrome

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Invitae

Jul 30, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.094

BayesDel_addAF

Benign

-0.25

BayesDel_noAF

Benign

-0.47

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.24

T;T

FATHMM_MKL

Uncertain

0.90

LIST_S2

Benign

0.84

T;D

M_CAP

Uncertain

0.11

MetaRNN

Benign

0.13

T;T

MetaSVM

Benign

-0.75

MutationAssessor

Benign

-0.77

N;.

MutationTaster

Benign

0.96

PrimateAI

Uncertain

0.53

PROVEAN

Benign

-1.0

N;.

REVEL

Benign

0.24

Sift

Benign

0.041

D;.

Sift4G

Uncertain

0.049

D;T

Polyphen

0.0

B;.

Vest4

0.20

MVP

0.67

MPC

1.4

ClinPred

0.27

GERP RS

4.4

Varity_R

0.35

gMVP

0.49

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over