rs10508796

Positions:

• chr10-34047269-G-A
• chr10-34047269-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 0.115 in 152,004 control chromosomes in the GnomAD database, including 3,129 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 0.12 (3129 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.381 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: 0.115 AC: 17490 AN: 151886 Hom.: 3116 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0459

Gnomad ASJ AF: 0.00317

Gnomad EAS AF: 0.000387

Gnomad SAS AF: 0.00436

Gnomad FIN AF: 0.00397

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.00869

Gnomad OTH AF: 0.0910

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

GnomAD4 genome AF: 0.115 AC: 17540 AN: 152004 Hom.: 3129 Cov.: 32 AF XY: 0.112 AC XY: 8294 AN XY: 74310

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.0458

Gnomad4 ASJ AF: 0.00317

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.00395

Gnomad4 FIN AF: 0.00397

Gnomad4 NFE AF: 0.00869

Gnomad4 OTH AF: 0.0900

Alfa AF: 0.0651 Hom.: 663

Bravo AF: 0.131

Asia WGS AF: 0.0280 AC: 99 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	13
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10508796; hg19: chr10-34336197;