rs7641536

Variant names:

• chr3-80354083-T-C
• rs7641536

Your query was ambiguous. Multiple possible variants found:

• chr3-80354083-T-C
• chr3-80354083-T-G

Variant summary

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

The variant allele was found at a frequency of 0.133 in 151,644 control chromosomes in the GnomAD database, including 2,403 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 0.13 (2403 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.548
• Publications: 0 publications found

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 (EAS) allele frequency at 95% confidence interval = 0.51 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

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20117 AN: 151528 Hom.: 2400 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.0643

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.0625

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0525

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.133 AC: 20148 AN: 151644 Hom.: 2403 Cov.: 32 AF XY: 0.136 AC XY: 10116 AN XY: 74124

African (AFR) AF: 0.229 AC: 9447 AN: 41238

American (AMR) AF: 0.166 AC: 2526 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.0643 AC: 223 AN: 3470

East Asian (EAS) AF: 0.526 AC: 2708 AN: 5144

South Asian (SAS) AF: 0.154 AC: 742 AN: 4826

European-Finnish (FIN) AF: 0.0625 AC: 661 AN: 10582

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

European-Non Finnish (NFE) AF: 0.0525 AC: 3563 AN: 67830

Other (OTH) AF: 0.117 AC: 247 AN: 2104

Alfa AF: 0.0743 Hom.: 345

Bravo AF: 0.148

Asia WGS AF: 0.279 AC: 966 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.2
DANN	Benign	0.62
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs7641536; hg19: chr3-80403233; COSMIC: COSV107175558;