9-17531970-T-C

Variant names:

• chr9-17531970-T-C
• rs2593371

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.210 AC: 8697 AN: 41490

American (AMR) AF: 0.699 AC: 10687 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.582 AC: 2020 AN: 3472

East Asian (EAS) AF: 0.928 AC: 4799 AN: 5172

South Asian (SAS) AF: 0.775 AC: 3723 AN: 4806

European-Finnish (FIN) AF: 0.693 AC: 7317 AN: 10552

Middle Eastern (MID) AF: 0.541 AC: 158 AN: 292

European-Non Finnish (NFE) AF: 0.666 AC: 45275 AN: 67992

Other (OTH) AF: 0.556 AC: 1170 AN: 2106

Alfa AF: 0.628 Hom.: 109852

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
PhyloP100		0.24

Splicing

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

Other links and lift over

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