9-4774015-C-T

Variant names:

• chr9-4774015-C-T
• rs296859

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 0.611 in 151,996 control chromosomes in the GnomAD database, including 29,391 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 0.61 (29391 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.771 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: 0.611 AC: 92745 AN: 151880 Hom.: 29346 Cov.: 31

Gnomad AFR AF: 0.778

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.747

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.611 AC: 92855 AN: 151996 Hom.: 29391 Cov.: 31 AF XY: 0.604 AC XY: 44888 AN XY: 74282

African (AFR) AF: 0.778 AC: 32284 AN: 41474

American (AMR) AF: 0.503 AC: 7675 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1575 AN: 3468

East Asian (EAS) AF: 0.747 AC: 3861 AN: 5170

South Asian (SAS) AF: 0.634 AC: 3054 AN: 4814

European-Finnish (FIN) AF: 0.494 AC: 5212 AN: 10540

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.550 AC: 37347 AN: 67948

Other (OTH) AF: 0.575 AC: 1213 AN: 2110

Alfa AF: 0.579 Hom.: 8682

Bravo AF: 0.619

Asia WGS AF: 0.686 AC: 2383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.016
DANN	Benign	0.22
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs296859; hg19: chr9-4774015; COSMIC: COSV74078997;