3-191648679-G-A

Variant names:

• chr3-191648679-G-A
• rs1916636

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 0.378 in 151,982 control chromosomes in the GnomAD database, including 12,860 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 0.38 (12860 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0210
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.629 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: 0.377 AC: 57298 AN: 151864 Hom.: 12827 Cov.: 32

Gnomad AFR AF: 0.635

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.188

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.378 AC: 57391 AN: 151982 Hom.: 12860 Cov.: 32 AF XY: 0.377 AC XY: 27964 AN XY: 74268

African (AFR) AF: 0.635 AC: 26326 AN: 41450

American (AMR) AF: 0.342 AC: 5223 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1016 AN: 3470

East Asian (EAS) AF: 0.390 AC: 2017 AN: 5166

South Asian (SAS) AF: 0.350 AC: 1684 AN: 4814

European-Finnish (FIN) AF: 0.252 AC: 2651 AN: 10534

Middle Eastern (MID) AF: 0.182 AC: 53 AN: 292

European-Non Finnish (NFE) AF: 0.259 AC: 17613 AN: 67966

Other (OTH) AF: 0.333 AC: 701 AN: 2106

Alfa AF: 0.299 Hom.: 22355

Bravo AF: 0.393

Asia WGS AF: 0.375 AC: 1306 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.49
PhyloP100		0.021

Splicing

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

Other links and lift over

dbSNP: rs1916636; hg19: chr3-191366468;