rs7652652

Variant names:

• chr3-83621817-C-G
• rs7652652

Your query was ambiguous. Multiple possible variants found:

• chr3-83621817-C-G
• chr3-83621817-C-T

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 0.0502 in 152,080 control chromosomes in the GnomAD database, including 279 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 0.050 (279 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.196
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0722 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: 0.0503 AC: 7639 AN: 151962 Hom.: 279 Cov.: 32

Gnomad AFR AF: 0.0122

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.0392

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.000194

Gnomad SAS AF: 0.0188

Gnomad FIN AF: 0.0721

Gnomad MID AF: 0.0641

Gnomad NFE AF: 0.0738

Gnomad OTH AF: 0.0654

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

GnomAD4 genome AF: 0.0502 AC: 7641 AN: 152080 Hom.: 279 Cov.: 32 AF XY: 0.0496 AC XY: 3684 AN XY: 74328

African (AFR) AF: 0.0122 AC: 505 AN: 41528

American (AMR) AF: 0.0392 AC: 597 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 353 AN: 3470

East Asian (EAS) AF: 0.000194 AC: 1 AN: 5148

South Asian (SAS) AF: 0.0186 AC: 90 AN: 4830

European-Finnish (FIN) AF: 0.0721 AC: 762 AN: 10574

Middle Eastern (MID) AF: 0.0690 AC: 20 AN: 290

European-Non Finnish (NFE) AF: 0.0739 AC: 5021 AN: 67966

Other (OTH) AF: 0.0647 AC: 137 AN: 2116

Alfa AF: 0.0290 Hom.: 15

Bravo AF: 0.0490

Asia WGS AF: 0.00982 AC: 34 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.44
DANN	Benign	0.43
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs7652652; hg19: chr3-83670968;