rs10972333

Positions:

• chr9-35136149-C-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 0.295 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;