rs10509967

Positions:

• chr10-112936173-A-C
• chr10-112936173-A-G
• chr10-112936173-A-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 0.224 in 152,064 control chromosomes in the GnomAD database, including 4,235 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 0.22 (4235 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.28 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: 0.224 AC: 34006 AN: 151946 Hom.: 4230 Cov.: 31

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.0630

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.224 AC: 34029 AN: 152064 Hom.: 4235 Cov.: 31 AF XY: 0.222 AC XY: 16527 AN XY: 74334

Gnomad4 AFR AF: 0.111

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.0633

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.264

Gnomad4 NFE AF: 0.283

Gnomad4 OTH AF: 0.237

Alfa AF: 0.221 Hom.: 1438

Bravo AF: 0.218

Asia WGS AF: 0.189 AC: 657 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	0.96
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10509967; hg19: chr10-114695932;