rs7246953

Variant names:

• chr19-10510432-G-A
• rs7246953

Your query was ambiguous. Multiple possible variants found:

• chr19-10510432-G-A
• chr19-10510432-G-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.193 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

Gnomad4 AFR AF: 0.219

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.183

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.195

Gnomad4 OTH AF: 0.193

Alfa AF: 0.188 Hom.: 5336

Bravo AF: 0.193

Asia WGS AF: 0.138 AC: 477 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7246953; hg19: chr19-10621108;