19-6941150-G-C

Variant names:

• chr19-6941150-G-C
• rs460375

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 0.696 in 151,884 control chromosomes in the GnomAD database, including 37,062 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 0.70 (37062 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.482
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.696 AC: 105693 AN: 151766 Hom.: 37043 Cov.: 30

Gnomad AFR AF: 0.617

Gnomad AMI AF: 0.897

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.726

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.685

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

GnomAD4 genome AF: 0.696 AC: 105752 AN: 151884 Hom.: 37062 Cov.: 30 AF XY: 0.696 AC XY: 51669 AN XY: 74230

African (AFR) AF: 0.617 AC: 25550 AN: 41390

American (AMR) AF: 0.704 AC: 10742 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.706 AC: 2449 AN: 3470

East Asian (EAS) AF: 0.686 AC: 3538 AN: 5154

South Asian (SAS) AF: 0.667 AC: 3206 AN: 4806

European-Finnish (FIN) AF: 0.726 AC: 7650 AN: 10532

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.738 AC: 50170 AN: 67962

Other (OTH) AF: 0.677 AC: 1426 AN: 2106

Alfa AF: 0.623 Hom.: 1804

Bravo AF: 0.693

Asia WGS AF: 0.617 AC: 2148 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	6.6
DANN	Benign	0.35
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs460375; hg19: chr19-6941161;