rs7614680

Variant names:

• chr3-189368253-C-A
• rs7614680

Your query was ambiguous. Multiple possible variants found:

• chr3-189368253-C-A
• chr3-189368253-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 0.236 in 151,750 control chromosomes in the GnomAD database, including 4,706 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 0.24 (4706 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35782 AN: 151632 Hom.: 4696 Cov.: 32

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.0381

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.236 AC: 35824 AN: 151750 Hom.: 4706 Cov.: 32 AF XY: 0.229 AC XY: 16984 AN XY: 74162

African (AFR) AF: 0.342 AC: 14122 AN: 41324

American (AMR) AF: 0.252 AC: 3841 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 798 AN: 3464

East Asian (EAS) AF: 0.0382 AC: 197 AN: 5156

South Asian (SAS) AF: 0.153 AC: 735 AN: 4808

European-Finnish (FIN) AF: 0.111 AC: 1166 AN: 10518

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.209 AC: 14211 AN: 67916

Other (OTH) AF: 0.249 AC: 526 AN: 2114

Alfa AF: 0.206 Hom.: 2811

Bravo AF: 0.254

Asia WGS AF: 0.106 AC: 368 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.55
DANN	Benign	0.21
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs7614680; hg19: chr3-189086042;