rs6510502

chr19-35647577-A-Cchr19-35647577-A-G

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 0.157 in 149,368 control chromosomes in the GnomAD database, including 2,016 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 0.16 (2016 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23404 AN: 149250 Hom.: 2009 Cov.: 30

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.0624

Gnomad EAS AF: 0.0736

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.0682

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.157 AC: 23444 AN: 149368 Hom.: 2016 Cov.: 30 AF XY: 0.158 AC XY: 11516 AN XY: 72892

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.0624

Gnomad4 EAS AF: 0.0738

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.163

Alfa AF: 0.120 Hom.: 1417

Bravo AF: 0.166

Asia WGS AF: 0.156 AC: 540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	2.5
Dann	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6510502; hg19: chr19-36138479; COSMIC: COSV55837000;