19-2947154-C-T

Variant names:

• chr19-2947154-C-T
• rs4806891

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 0.828 in 151,866 control chromosomes in the GnomAD database, including 52,422 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 0.83 (52422 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.89 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: 0.828 AC: 125715 AN: 151748 Hom.: 52390 Cov.: 32

Gnomad AFR AF: 0.898

Gnomad AMI AF: 0.956

Gnomad AMR AF: 0.813

Gnomad ASJ AF: 0.811

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.708

Gnomad FIN AF: 0.849

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.805

Gnomad OTH AF: 0.819

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

GnomAD4 genome AF: 0.828 AC: 125798 AN: 151866 Hom.: 52422 Cov.: 32 AF XY: 0.829 AC XY: 61564 AN XY: 74220

African (AFR) AF: 0.898 AC: 37069 AN: 41278

American (AMR) AF: 0.812 AC: 12387 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.811 AC: 2813 AN: 3468

East Asian (EAS) AF: 0.688 AC: 3548 AN: 5158

South Asian (SAS) AF: 0.708 AC: 3416 AN: 4826

European-Finnish (FIN) AF: 0.849 AC: 8982 AN: 10580

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.805 AC: 54768 AN: 67994

Other (OTH) AF: 0.816 AC: 1722 AN: 2110

Alfa AF: 0.809 Hom.: 145508

Bravo AF: 0.829

Asia WGS AF: 0.695 AC: 2419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.97
DANN	Benign	0.26
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs4806891; hg19: chr19-2947152;