rs10509967

Variant names:

• chr10-112936173-A-C
• rs10509967

Your query was ambiguous. Multiple possible variants found:

• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;