rs10507846

chr13-76036704-T-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 0.0866 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;