rs10507846

Variant names:

• chr13-76036704-T-C
• rs10507846

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 0.0866 in 151,928 control chromosomes in the GnomAD database, including 655 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 0.087 (655 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.35

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.116 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: 0.0867 AC: 13160 AN: 151810 Hom.: 656 Cov.: 32

Gnomad AFR AF: 0.0681

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.0805

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.0386

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.0711

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0979

Gnomad OTH AF: 0.0972

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

GnomAD4 genome AF: 0.0866 AC: 13161 AN: 151928 Hom.: 655 Cov.: 32 AF XY: 0.0855 AC XY: 6348 AN XY: 74260

Gnomad4 AFR AF: 0.0681

Gnomad4 AMR AF: 0.0804

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.0387

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.0711

Gnomad4 NFE AF: 0.0980

Gnomad4 OTH AF: 0.0967

Alfa AF: 0.102 Hom.: 1106

Bravo AF: 0.0871

Asia WGS AF: 0.0970 AC: 340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	11
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10507846; hg19: chr13-76610840;