19-7671913-A-T

Variant names:

• chr19-7671913-A-T
• rs1477341

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 0.437 in 152,046 control chromosomes in the GnomAD database, including 17,052 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 0.44 (17052 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.556
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66492 AN: 151928 Hom.: 17041 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.700

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.437 AC: 66513 AN: 152046 Hom.: 17052 Cov.: 32 AF XY: 0.444 AC XY: 33011 AN XY: 74314

African (AFR) AF: 0.154 AC: 6404 AN: 41478

American (AMR) AF: 0.424 AC: 6468 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.611 AC: 2119 AN: 3470

East Asian (EAS) AF: 0.509 AC: 2633 AN: 5170

South Asian (SAS) AF: 0.702 AC: 3386 AN: 4826

European-Finnish (FIN) AF: 0.602 AC: 6362 AN: 10570

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.552 AC: 37542 AN: 67952

Other (OTH) AF: 0.482 AC: 1020 AN: 2114

Alfa AF: 0.348 Hom.: 1059

Bravo AF: 0.410

Asia WGS AF: 0.577 AC: 2006 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
DANN	Benign	0.78
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs1477341; hg19: chr19-7736799;