rs10967875

Variant names:

• chr9-27309661-T-C
• rs10967875

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 0.214 in 152,072 control chromosomes in the GnomAD database, including 4,229 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 0.21 (4229 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.475

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.292 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: 0.214 AC: 32470 AN: 151954 Hom.: 4218 Cov.: 32

Gnomad AFR AF: 0.0553

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.214 AC: 32498 AN: 152072 Hom.: 4229 Cov.: 32 AF XY: 0.212 AC XY: 15786 AN XY: 74332

Gnomad4 AFR AF: 0.0553

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.196

Gnomad4 NFE AF: 0.282

Gnomad4 OTH AF: 0.266

Alfa AF: 0.284 Hom.: 12950

Bravo AF: 0.215

Asia WGS AF: 0.258 AC: 897 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.2
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10967875; hg19: chr9-27309659;