9-17531970-T-C

Variant names:

• chr9-17531970-T-C
• rs2593371

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 0.555 in 152,076 control chromosomes in the GnomAD database, including 27,180 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 0.55 (27180 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.242

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.906 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: 0.555 AC: 84387 AN: 151958 Hom.: 27174 Cov.: 32

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.928

Gnomad SAS AF: 0.775

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.555 AC: 84398 AN: 152076 Hom.: 27180 Cov.: 32 AF XY: 0.566 AC XY: 42074 AN XY: 74330

Gnomad4 AFR AF: 0.210

Gnomad4 AMR AF: 0.699

Gnomad4 ASJ AF: 0.582

Gnomad4 EAS AF: 0.928

Gnomad4 SAS AF: 0.775

Gnomad4 FIN AF: 0.693

Gnomad4 NFE AF: 0.666

Gnomad4 OTH AF: 0.556

Alfa AF: 0.647 Hom.: 47391

Bravo AF: 0.540

Asia WGS AF: 0.769 AC: 2672 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.2
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2593371; hg19: chr9-17531968; COSMIC: COSV60336278;