rs7743761

Variant names:

• chr6-31368323-C-A
• rs7743761
• ENST00000649421.2:n.274+993C>A

Variant summary

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

The ENST00000649421.2(ENSG00000285647):​n.274+993C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 152,000 control chromosomes in the GnomAD database, including 8,094 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 0.31 (8094 hom., cov: 32)
• Consequence: ENSG00000285647 ENST00000649421.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.259
• Publications: 46 publications found

Genes affected

ENSG00000285647 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285647	ENST00000649421.2	n.274+993C>A		intron_variant	Intron 1 of 1
ENSG00000298426	ENST00000755446.1	n.327-13657C>A		intron_variant	Intron 1 of 1
ENSG00000285647	ENST00000755530.1	n.203-6560C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47612 AN: 151882 Hom.: 8067 Cov.: 32

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.314 AC: 47684 AN: 152000 Hom.: 8094 Cov.: 32 AF XY: 0.322 AC XY: 23932 AN XY: 74300

African (AFR) AF: 0.348 AC: 14436 AN: 41426

American (AMR) AF: 0.425 AC: 6499 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.538 AC: 1867 AN: 3470

East Asian (EAS) AF: 0.341 AC: 1767 AN: 5180

South Asian (SAS) AF: 0.368 AC: 1777 AN: 4832

European-Finnish (FIN) AF: 0.361 AC: 3805 AN: 10544

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16426 AN: 67946

Other (OTH) AF: 0.328 AC: 692 AN: 2108

Alfa AF: 0.266 Hom.: 18930

Bravo AF: 0.317

Asia WGS AF: 0.385 AC: 1341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.8
DANN	Benign	0.79
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs7743761; hg19: chr6-31336100;