chr7-151253854-G-A

Variant names:

• chr7-151253854-G-A
• rs7781265
• ENST00000356800.6:c.40-8183C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000356800.6(SMARCD3):​c.40-8183C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 151,736 control chromosomes in the GnomAD database, including 2,273 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.15 (2273 hom., cov: 33)
• Consequence: SMARCD3 ENST00000356800.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.886
• Publications: 11 publications found

Genes affected

SMARCD3 (HGNC:11108): (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3) The protein encoded by this gene is a member of the SWI/SNF family of proteins, whose members display helicase and ATPase activities and which are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. The encoded protein is part of the large ATP-dependent chromatin remodeling complex SNF/SWI and has sequence similarity to the yeast Swp73 protein. Multiple alternatively spliced transcript variants have been found for this gene, but the biological validity of some variants has not been determined. [provided by RefSeq, Jul 2008]

ENSG00000243018 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SMARCD3	NM_001003802.2	c.40-8183C>T		intron_variant	Intron 2 of 13		NP_001003802.1
SMARCD3	NM_003078.4	c.40-8183C>T		intron_variant	Intron 2 of 13		NP_003069.2
SMARCD3	XM_047420758.1	c.-16-10153C>T		intron_variant	Intron 1 of 11		XP_047276714.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMARCD3	ENST00000356800.6	c.40-8183C>T		intron_variant	Intron 2 of 13	1		ENSP00000349254.2
SMARCD3	ENST00000392811.6	c.40-8183C>T		intron_variant	Intron 2 of 13	1		ENSP00000376558.2
SMARCD3	ENST00000491651.1	c.40-8183C>T		intron_variant	Intron 2 of 4	4		ENSP00000419886.1

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22850 AN: 151618 Hom.: 2261 Cov.: 33

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.0286

Gnomad AMR AF: 0.0843

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.00136

Gnomad SAS AF: 0.0878

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.151 AC: 22895 AN: 151736 Hom.: 2273 Cov.: 33 AF XY: 0.147 AC XY: 10936 AN XY: 74158

African (AFR) AF: 0.284 AC: 11742 AN: 41308

American (AMR) AF: 0.0841 AC: 1282 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.100 AC: 347 AN: 3464

East Asian (EAS) AF: 0.00137 AC: 7 AN: 5128

South Asian (SAS) AF: 0.0875 AC: 420 AN: 4800

European-Finnish (FIN) AF: 0.109 AC: 1147 AN: 10552

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7629 AN: 67932

Other (OTH) AF: 0.125 AC: 264 AN: 2110

Alfa AF: 0.137 Hom.: 213

Bravo AF: 0.154

Asia WGS AF: 0.0590 AC: 208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.17
DANN	Benign	0.61
PhyloP100		-0.89
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs7781265; hg19: chr7-150950940;