rs7611677

Variant names:

• chr3-42235432-G-A
• rs7611677

Your query was ambiguous. Multiple possible variants found:

• chr3-42235432-G-A
• chr3-42235432-G-C

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 0.169 in 152,050 control chromosomes in the GnomAD database, including 4,169 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 0.17 (4169 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.355
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25603 AN: 151932 Hom.: 4158 Cov.: 32

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.00659

Gnomad AMR AF: 0.0915

Gnomad ASJ AF: 0.0738

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0627

Gnomad FIN AF: 0.0645

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0743

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.169 AC: 25648 AN: 152050 Hom.: 4169 Cov.: 32 AF XY: 0.163 AC XY: 12113 AN XY: 74330

African (AFR) AF: 0.425 AC: 17616 AN: 41420

American (AMR) AF: 0.0913 AC: 1396 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0738 AC: 256 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5178

South Asian (SAS) AF: 0.0630 AC: 303 AN: 4812

European-Finnish (FIN) AF: 0.0645 AC: 682 AN: 10578

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0743 AC: 5053 AN: 67988

Other (OTH) AF: 0.143 AC: 302 AN: 2112

Alfa AF: 0.125 Hom.: 298

Bravo AF: 0.182

Asia WGS AF: 0.0610 AC: 213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	7.5
DANN	Benign	0.92
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs7611677; hg19: chr3-42276924;