chr19-40976837-C-T

Variant names:

• chr19-40976837-C-T
• rs7251950

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 0.29 in 151,924 control chromosomes in the GnomAD database, including 7,340 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 0.29 (7340 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0170
• Publications: 11 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 (EAS) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44072 AN: 151806 Hom.: 7340 Cov.: 31

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.290 AC: 44088 AN: 151924 Hom.: 7340 Cov.: 31 AF XY: 0.297 AC XY: 22045 AN XY: 74238

African (AFR) AF: 0.136 AC: 5631 AN: 41398

American (AMR) AF: 0.355 AC: 5413 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1121 AN: 3472

East Asian (EAS) AF: 0.466 AC: 2411 AN: 5172

South Asian (SAS) AF: 0.348 AC: 1673 AN: 4810

European-Finnish (FIN) AF: 0.431 AC: 4547 AN: 10554

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.328 AC: 22286 AN: 67952

Other (OTH) AF: 0.299 AC: 629 AN: 2106

Alfa AF: 0.304 Hom.: 5742

Bravo AF: 0.281

Asia WGS AF: 0.374 AC: 1302 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.2
DANN	Benign	0.61
PhyloP100		0.017

Splicing

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

Other links and lift over

dbSNP: rs7251950; hg19: chr19-41482742;