rs764681

Variant names:

• chr16-8433773-C-T
• rs764681
• ENST00000787385.1:n.211-1804C>T

Variant summary

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

The ENST00000787385.1(ENSG00000302503):​n.211-1804C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 151,998 control chromosomes in the GnomAD database, including 8,243 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 (8243 hom., cov: 32)
• Consequence: ENSG00000302503 ENST00000787385.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.159
• Publications: 3 publications found

Genes affected

ENSG00000302503 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.501 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
ENSG00000302503	ENST00000787385.1	n.211-1804C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47754 AN: 151880 Hom.: 8227 Cov.: 32

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.315 AC: 47804 AN: 151998 Hom.: 8243 Cov.: 32 AF XY: 0.317 AC XY: 23569 AN XY: 74298

African (AFR) AF: 0.360 AC: 14922 AN: 41436

American (AMR) AF: 0.457 AC: 6967 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1311 AN: 3470

East Asian (EAS) AF: 0.518 AC: 2675 AN: 5166

South Asian (SAS) AF: 0.354 AC: 1707 AN: 4818

European-Finnish (FIN) AF: 0.194 AC: 2051 AN: 10580

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.250 AC: 17000 AN: 67958

Other (OTH) AF: 0.352 AC: 742 AN: 2110

Alfa AF: 0.278 Hom.: 26696

Bravo AF: 0.340

Asia WGS AF: 0.470 AC: 1630 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.6
DANN	Benign	0.55
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs764681; hg19: chr16-8483775;