Variant 4-94276369-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_020159.5(SMARCAD1):c.1839C>T(p.Asp613=) 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

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 id is 1236001.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr4-94276369-C-T is described in Lovd as [Benign].

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/exons	MANE	UniProt
SMARCAD1	NM_020159.5 linkuse as main transcript	c.1839C>T	p.Asp613=	synonymous_variant	15/24	ENST00000354268.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SMARCAD1	ENST00000354268.9 linkuse as main transcript	c.1839C>T	p.Asp613=	synonymous_variant	15/24	1	NM_020159.5	P4	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

GnomAD3 exomes

AF:

0.598

AC:

150244

AN:

251080

Hom.:

45940

AF XY:

0.598

AC XY:

81202

AN XY:

135682

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 SAS exome

AF:

0.633

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

Gnomad4 AFR exome

AF:

0.369

Gnomad4 AMR exome

AF:

0.708

Gnomad4 ASJ exome

AF:

0.521

Gnomad4 EAS exome

AF:

0.757

Gnomad4 SAS exome

AF:

0.629

Gnomad4 FIN exome

AF:

0.575

Gnomad4 NFE exome

AF:

0.582

Gnomad4 OTH exome

AF:

0.573

GnomAD4 genome

AF:

0.534

AC:

81159

AN:

151994

Hom.:

22419

Cov.:

AF XY:

0.540

AC XY:

40094

AN XY:

74286

show subpopulations

Gnomad4 AFR

AF:

0.378

Gnomad4 AMR

AF:

0.620

Gnomad4 ASJ

AF:

0.525

Gnomad4 EAS

AF:

0.715

Gnomad4 SAS

AF:

0.630

Gnomad4 FIN

AF:

0.571

Gnomad4 NFE

AF:

0.583

Gnomad4 OTH

AF:

0.528

Alfa

AF:

0.567

Hom.:

34205

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

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	- -

Keratoderma with scleroatrophy of the extremities

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 15, 2021

- -

Basan syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 15, 2021

- -

Adermatoglyphia

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.37

CADD

Benign

7.3

DANN

Benign

0.69

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

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