4-94241274-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_020159.5(SMARCAD1):c.705+268G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 151,996 control chromosomes in the GnomAD database, including 28,807 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.61 (28807 hom., cov: 32)
• Consequence: SMARCAD1 NM_020159.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.12

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BP6: Variant 4-94241274-G-A is Benign according to our data. Variant chr4-94241274-G-A is described in ClinVar as [Benign]. Clinvar id is 1283015.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.7 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SMARCAD1	NM_020159.5	c.705+268G>A		intron_variant		ENST00000354268.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SMARCAD1	ENST00000354268.9	c.705+268G>A		intron_variant		1	NM_020159.5	P4

Frequencies

GnomAD3 genomes AF: 0.614 AC: 93316 AN: 151878 Hom.: 28775 Cov.: 32

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.720

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.588

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.615 AC: 93404 AN: 151996 Hom.: 28807 Cov.: 32 AF XY: 0.618 AC XY: 45909 AN XY: 74300

Gnomad4 AFR AF: 0.646

Gnomad4 AMR AF: 0.657

Gnomad4 ASJ AF: 0.535

Gnomad4 EAS AF: 0.720

Gnomad4 SAS AF: 0.637

Gnomad4 FIN AF: 0.573

Gnomad4 NFE AF: 0.587

Gnomad4 OTH AF: 0.595

Alfa AF: 0.605 Hom.: 3470

Bravo AF: 0.622

Asia WGS AF: 0.684 AC: 2381 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.21
Dann	Benign	0.16

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

Other links and lift over

dbSNP: rs12511433; hg19: chr4-95162425;