rs7630698

Variant names:

• chr3-189482141-A-C
• rs7630698

Your query was ambiguous. Multiple possible variants found:

• chr3-189482141-A-C
• chr3-189482141-A-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 0.466 in 152,186 control chromosomes in the GnomAD database, including 17,626 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 (17626 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.642
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.57 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: 0.466 AC: 70840 AN: 152068 Hom.: 17614 Cov.: 34

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.466 AC: 70898 AN: 152186 Hom.: 17626 Cov.: 34 AF XY: 0.464 AC XY: 34507 AN XY: 74404

African (AFR) AF: 0.313 AC: 13005 AN: 41522

American (AMR) AF: 0.468 AC: 7149 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1632 AN: 3472

East Asian (EAS) AF: 0.173 AC: 896 AN: 5186

South Asian (SAS) AF: 0.375 AC: 1811 AN: 4824

European-Finnish (FIN) AF: 0.538 AC: 5691 AN: 10582

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.575 AC: 39095 AN: 67998

Other (OTH) AF: 0.478 AC: 1010 AN: 2114

Alfa AF: 0.533 Hom.: 99167

Bravo AF: 0.451

Asia WGS AF: 0.286 AC: 994 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	10
DANN	Benign	0.94
PhyloP100		0.64

Splicing

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

Other links and lift over

dbSNP: rs7630698; hg19: chr3-189199930;