rs7702276

Variant names:

• chr5-52509908-C-T
• rs7702276

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 0.468 in 151,880 control chromosomes in the GnomAD database, including 18,323 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 0.47 (18323 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.390
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.7 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: 0.467 AC: 70929 AN: 151762 Hom.: 18278 Cov.: 32

Gnomad AFR AF: 0.706

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.468 AC: 71028 AN: 151880 Hom.: 18323 Cov.: 32 AF XY: 0.466 AC XY: 34603 AN XY: 74206

African (AFR) AF: 0.706 AC: 29271 AN: 41442

American (AMR) AF: 0.442 AC: 6742 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 1275 AN: 3466

East Asian (EAS) AF: 0.405 AC: 2087 AN: 5148

South Asian (SAS) AF: 0.481 AC: 2316 AN: 4810

European-Finnish (FIN) AF: 0.342 AC: 3604 AN: 10542

Middle Eastern (MID) AF: 0.346 AC: 101 AN: 292

European-Non Finnish (NFE) AF: 0.359 AC: 24405 AN: 67914

Other (OTH) AF: 0.438 AC: 922 AN: 2106

Alfa AF: 0.422 Hom.: 22375

Bravo AF: 0.485

Asia WGS AF: 0.503 AC: 1748 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.20
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs7702276; hg19: chr5-51805742; COSMIC: COSV107162796;