19-10510432-G-A

Variant names:

• chr19-10510432-G-A
• rs7246953

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 0.193 in 152,160 control chromosomes in the GnomAD database, including 2,940 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 0.19 (2940 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.216 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: 0.193 AC: 29288 AN: 152040 Hom.: 2941 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.193 AC: 29300 AN: 152160 Hom.: 2940 Cov.: 32 AF XY: 0.190 AC XY: 14124 AN XY: 74388

African (AFR) AF: 0.219 AC: 9109 AN: 41514

American (AMR) AF: 0.139 AC: 2125 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 606 AN: 3468

East Asian (EAS) AF: 0.183 AC: 946 AN: 5178

South Asian (SAS) AF: 0.143 AC: 690 AN: 4826

European-Finnish (FIN) AF: 0.175 AC: 1854 AN: 10590

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.195 AC: 13270 AN: 67980

Other (OTH) AF: 0.193 AC: 408 AN: 2114

Alfa AF: 0.191 Hom.: 11793

Bravo AF: 0.193

Asia WGS AF: 0.138 AC: 477 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.014
DANN	Benign	0.74
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs7246953; hg19: chr19-10621108;