rs10507556

Variant names:

• chr13-47395940-G-A
• rs10507556

Your query was ambiguous. Multiple possible variants found:

• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;