9-1162556-T-C

Variant names:

• chr9-1162556-T-C
• rs7028761

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 0.516 in 151,958 control chromosomes in the GnomAD database, including 20,897 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 0.52 (20897 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.526
• 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 = 0.735 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: 0.516 AC: 78344 AN: 151840 Hom.: 20865 Cov.: 33

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.755

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.516 AC: 78429 AN: 151958 Hom.: 20897 Cov.: 33 AF XY: 0.526 AC XY: 39045 AN XY: 74286

African (AFR) AF: 0.583 AC: 24148 AN: 41452

American (AMR) AF: 0.551 AC: 8393 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1324 AN: 3468

East Asian (EAS) AF: 0.755 AC: 3906 AN: 5172

South Asian (SAS) AF: 0.580 AC: 2793 AN: 4816

European-Finnish (FIN) AF: 0.614 AC: 6487 AN: 10572

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.439 AC: 29832 AN: 67922

Other (OTH) AF: 0.505 AC: 1065 AN: 2108

Alfa AF: 0.405 Hom.: 1796

Bravo AF: 0.514

Asia WGS AF: 0.693 AC: 2407 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	4.2
DANN	Benign	0.76
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs7028761; hg19: chr9-1162556; COSMIC: COSV70075739;