rs10972333

Variant names:

• chr9-35136149-C-T
• rs10972333

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 0.295 in 152,186 control chromosomes in the GnomAD database, including 8,347 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 0.30 (8347 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.394 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: 0.296 AC: 44948 AN: 152068 Hom.: 8339 Cov.: 33

Gnomad AFR AF: 0.0975

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.00558

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.295 AC: 44962 AN: 152186 Hom.: 8347 Cov.: 33 AF XY: 0.292 AC XY: 21735 AN XY: 74380

Gnomad4 AFR AF: 0.0974

Gnomad4 AMR AF: 0.398

Gnomad4 ASJ AF: 0.351

Gnomad4 EAS AF: 0.00579

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.435

Gnomad4 NFE AF: 0.398

Gnomad4 OTH AF: 0.323

Alfa AF: 0.355 Hom.: 1843

Bravo AF: 0.285

Asia WGS AF: 0.104 AC: 364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.3
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10972333; hg19: chr9-35136146; COSMIC: COSV60353549;