rs6823404

Variant names:

Variant summary

Our verdict is Benign. The variant received -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_020159.5(SMARCAD1):c.1839C>T(p.Asp613Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.582 in 1,613,358 control chromosomes in the GnomAD database, including 276,412 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.53 ( 22419 hom., cov: 32)

Exomes 𝑓: 0.59 ( 253993 hom. )

Consequence

SMARCAD1
NM_020159.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -0.0790

Publications

29 publications found

Variant links:

Genes affected

SMARCAD1 (HGNC:18398): (SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1) This gene encodes a member of the SNF subfamily of helicase proteins. The encoded protein plays a critical role in the restoration of heterochromatin organization and propagation of epigenetic patterns following DNA replication by mediating histone H3/H4 deacetylation. Mutations in this gene are associated with adermatoglyphia. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2011]

SMARCAD1 Gene-Disease associations (from GenCC):

ectodermal dysplasia syndrome
Inheritance: AD Classification: DEFINITIVE Submitted by: Illumina
isolated congenital adermatoglyphia
Inheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet
palmoplantar keratoderma-sclerodactyly syndrome
Inheritance: AD Classification: MODERATE, SUPPORTIVE Submitted by: G2P, Orphanet
absence of fingerprints-congenital milia syndrome
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

SMARCAD1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.37).

BP6

Variant 4-94276369-C-T is Benign according to our data. Variant chr4-94276369-C-T is described in ClinVar as Benign. ClinVar VariationId is 1236001.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.079 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SMARCAD1	NM_020159.5 link	c.1839C>T	p.Asp613Asp	synonymous_variant	Exon 15 of 24	ENST00000354268.9	NP_064544.2	Q9H4L7-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMARCAD1	ENST00000354268.9 link	c.1839C>T	p.Asp613Asp	synonymous_variant	Exon 15 of 24	1	NM_020159.5	ENSP00000346217.4		Q9H4L7-1

Frequencies

GnomAD3 genomes

AF:

0.534

AC:

81111

AN:

151876

Hom.:

22409

Cov.:

show subpopulations

Gnomad AFR

AF:

0.379

Gnomad AMI

AF:

0.612

Gnomad AMR

AF:

0.619

Gnomad ASJ

AF:

0.525

Gnomad EAS

AF:

0.715

Gnomad SAS

AF:

0.631

Gnomad FIN

AF:

0.571

Gnomad MID

AF:

0.544

Gnomad NFE

AF:

0.583

Gnomad OTH

AF:

0.522

GnomAD2 exomes

AF:

0.598

AC:

150244

AN:

251080

AF XY:

0.598

show subpopulations

Gnomad AFR exome

AF:

0.370

Gnomad AMR exome

AF:

0.718

Gnomad ASJ exome

AF:

0.527

Gnomad EAS exome

AF:

0.708

Gnomad FIN exome

AF:

0.580

Gnomad NFE exome

AF:

0.579

Gnomad OTH exome

AF:

0.577

GnomAD4 exome

AF:

0.587

AC:

857157

AN:

1461364

Hom.:

253993

Cov.:

AF XY:

0.588

AC XY:

427212

AN XY:

726998

show subpopulations

African (AFR)

AF:

0.369

AC:

12352

AN:

33476

American (AMR)

AF:

0.708

AC:

31644

AN:

44712

Ashkenazi Jewish (ASJ)

AF:

0.521

AC:

13620

AN:

26128

East Asian (EAS)

AF:

0.757

AC:

30022

AN:

39678

South Asian (SAS)

AF:

0.629

AC:

54250

AN:

86230

European-Finnish (FIN)

AF:

0.575

AC:

30716

AN:

53374

Middle Eastern (MID)

AF:

0.543

AC:

3130

AN:

5764

European-Non Finnish (NFE)

AF:

0.582

AC:

646853

AN:

1111626

Other (OTH)

AF:

0.573

AC:

34570

AN:

60376

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.471

Heterozygous variant carriers

18807

37613

56420

75226

94033

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

17838

35676

53514

71352

89190

<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:

0.534

AC:

81159

AN:

151994

Hom.:

22419

Cov.:

AF XY:

0.540

AC XY:

40094

AN XY:

74286

show subpopulations

African (AFR)

AF:

0.378

AC:

15680

AN:

41448

American (AMR)

AF:

0.620

AC:

9461

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.525

AC:

1822

AN:

3472

East Asian (EAS)

AF:

0.715

AC:

3687

AN:

5160

South Asian (SAS)

AF:

0.630

AC:

3040

AN:

4822

European-Finnish (FIN)

AF:

0.571

AC:

6015

AN:

10538

Middle Eastern (MID)

AF:

0.537

AC:

158

AN:

294

European-Non Finnish (NFE)

AF:

0.583

AC:

39623

AN:

67970

Other (OTH)

AF:

0.528

AC:

1116

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1881

3763

5644

7526

9407

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

720

1440

2160

2880

3600

<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:

0.566

Hom.:

45739

Bravo

AF:

0.530

Asia WGS

AF:

0.667

AC:

2320

AN:

3478

EpiCase

AF:

0.570

EpiControl

AF:

0.567

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Nov 12, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Keratoderma with scleroatrophy of the extremities

Benign:1

Jul 15, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Basan syndrome

Benign:1

Jul 15, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Adermatoglyphia

Benign:1

Jul 15, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.37

CADD

Benign

7.3

(source)

DANN

Benign

0.69

PhyloP100

-0.079

Mutation Taster

=83/17

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over