rs7781265

Positions:

• chr7-151253854-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000466775.1(ENSG00000243018):​n.139-459G>A variant causes a intron, non coding transcript 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: ENST00000466775.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.886

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
SMARCD3	NM_001003802.2	c.40-8183C>T		intron_variant			NP_001003802.1
SMARCD3	NM_003078.4	c.40-8183C>T		intron_variant			NP_003069.2
SMARCD3	XM_047420758.1	c.-16-10153C>T		intron_variant			XP_047276714.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000466775.1	n.139-459G>A		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.284

Gnomad4 AMR AF: 0.0841

Gnomad4 ASJ AF: 0.100

Gnomad4 EAS AF: 0.00137

Gnomad4 SAS AF: 0.0875

Gnomad4 FIN AF: 0.109

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.125

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7781265; hg19: chr7-150950940;