19-10482961-C-T

Variant names:

• chr19-10482961-C-T
• rs34197572

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 0.0522 in 151,668 control chromosomes in the GnomAD database, including 347 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 0.052 (347 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.167
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0693 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: 0.0523 AC: 7919 AN: 151550 Hom.: 347 Cov.: 29

Gnomad AFR AF: 0.0134

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.0465

Gnomad ASJ AF: 0.0671

Gnomad EAS AF: 0.000780

Gnomad SAS AF: 0.0189

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0709

Gnomad OTH AF: 0.0529

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

GnomAD4 genome AF: 0.0522 AC: 7915 AN: 151668 Hom.: 347 Cov.: 29 AF XY: 0.0531 AC XY: 3930 AN XY: 74076

African (AFR) AF: 0.0134 AC: 556 AN: 41480

American (AMR) AF: 0.0464 AC: 706 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.0671 AC: 233 AN: 3470

East Asian (EAS) AF: 0.000782 AC: 4 AN: 5116

South Asian (SAS) AF: 0.0191 AC: 92 AN: 4808

European-Finnish (FIN) AF: 0.128 AC: 1321 AN: 10296

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0709 AC: 4822 AN: 67964

Other (OTH) AF: 0.0524 AC: 110 AN: 2100

Alfa AF: 0.0431 Hom.: 35

Bravo AF: 0.0461

Asia WGS AF: 0.0130 AC: 46 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.0
DANN	Benign	0.59
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs34197572; hg19: chr19-10593637;