9-13051713-C-T

Variant names:

• chr9-13051713-C-T
• rs2009991

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 0.336 in 152,026 control chromosomes in the GnomAD database, including 10,275 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 0.34 (10275 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.652
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.637 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: 0.336 AC: 51003 AN: 151908 Hom.: 10274 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.336 AC: 51014 AN: 152026 Hom.: 10275 Cov.: 32 AF XY: 0.343 AC XY: 25503 AN XY: 74300

African (AFR) AF: 0.110 AC: 4577 AN: 41508

American (AMR) AF: 0.433 AC: 6610 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.375 AC: 1300 AN: 3464

East Asian (EAS) AF: 0.656 AC: 3378 AN: 5152

South Asian (SAS) AF: 0.290 AC: 1401 AN: 4828

European-Finnish (FIN) AF: 0.490 AC: 5159 AN: 10536

Middle Eastern (MID) AF: 0.360 AC: 105 AN: 292

European-Non Finnish (NFE) AF: 0.401 AC: 27280 AN: 67952

Other (OTH) AF: 0.348 AC: 734 AN: 2110

Alfa AF: 0.381 Hom.: 7464

Bravo AF: 0.325

Asia WGS AF: 0.412 AC: 1433 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.6
DANN	Benign	0.64
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs2009991; hg19: chr9-13051712; COSMIC: COSV60332304;