19-10131268-C-T

Variant names:

• chr19-10131268-C-T
• rs4804122

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 0.607 in 151,728 control chromosomes in the GnomAD database, including 28,405 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 0.61 (28405 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.763
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.705 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: 0.607 AC: 92023 AN: 151610 Hom.: 28369 Cov.: 31

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.607 AC: 92118 AN: 151728 Hom.: 28405 Cov.: 31 AF XY: 0.611 AC XY: 45312 AN XY: 74156

African (AFR) AF: 0.666 AC: 27569 AN: 41382

American (AMR) AF: 0.698 AC: 10618 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1909 AN: 3470

East Asian (EAS) AF: 0.724 AC: 3725 AN: 5142

South Asian (SAS) AF: 0.680 AC: 3268 AN: 4808

European-Finnish (FIN) AF: 0.534 AC: 5627 AN: 10532

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.552 AC: 37452 AN: 67870

Other (OTH) AF: 0.622 AC: 1313 AN: 2110

Alfa AF: 0.583 Hom.: 33699

Bravo AF: 0.626

Asia WGS AF: 0.681 AC: 2370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.20
DANN	Benign	0.37
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs4804122; hg19: chr19-10241944;