9-22134173-C-T

Variant names:

• chr9-22134173-C-T
• rs10757283

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 0.451 in 151,976 control chromosomes in the GnomAD database, including 15,582 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 0.45 (15582 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.58

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.604 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: 0.451 AC: 68532 AN: 151858 Hom.: 15561 Cov.: 32

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.451 AC: 68593 AN: 151976 Hom.: 15582 Cov.: 32 AF XY: 0.453 AC XY: 33625 AN XY: 74272

Gnomad4 AFR AF: 0.468

Gnomad4 AMR AF: 0.431

Gnomad4 ASJ AF: 0.459

Gnomad4 EAS AF: 0.622

Gnomad4 SAS AF: 0.441

Gnomad4 FIN AF: 0.471

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.472

Alfa AF: 0.446 Hom.: 27587

Bravo AF: 0.452

Asia WGS AF: 0.550 AC: 1914 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.082
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10757283; hg19: chr9-22134172; COSMIC: COSV60341848;