rs10507556

Positions:

• chr13-47395940-G-A
• chr13-47395940-G-T

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 0.199 in 151,966 control chromosomes in the GnomAD database, including 4,131 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 0.20 (4131 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.197

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30239 AN: 151848 Hom.: 4123 Cov.: 32

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.0448

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.199 AC: 30277 AN: 151966 Hom.: 4131 Cov.: 32 AF XY: 0.197 AC XY: 14617 AN XY: 74258

Gnomad4 AFR AF: 0.393

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.153

Gnomad4 EAS AF: 0.0449

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.188

Alfa AF: 0.124 Hom.: 709

Bravo AF: 0.210

Asia WGS AF: 0.147 AC: 510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10507556; hg19: chr13-47970075;