19-6941150-G-C

Position:

• chr19-6941150-G-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.617

Gnomad4 AMR AF: 0.704

Gnomad4 ASJ AF: 0.706

Gnomad4 EAS AF: 0.686

Gnomad4 SAS AF: 0.667

Gnomad4 FIN AF: 0.726

Gnomad4 NFE AF: 0.738

Gnomad4 OTH AF: 0.677

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	6.6
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs460375; hg19: chr19-6941161;