9-21184476-C-G

Variant names:

• chr9-21184476-C-G
• rs4568676

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 0.362 in 147,828 control chromosomes in the GnomAD database, including 9,885 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 0.36 (9885 hom., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.79
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.09).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.506 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: 0.362 AC: 53468 AN: 147712 Hom.: 9881 Cov.: 23

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.362 AC: 53494 AN: 147828 Hom.: 9885 Cov.: 23 AF XY: 0.362 AC XY: 26062 AN XY: 71906

African (AFR) AF: 0.305 AC: 12126 AN: 39740

American (AMR) AF: 0.348 AC: 5103 AN: 14650

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 1230 AN: 3452

East Asian (EAS) AF: 0.326 AC: 1655 AN: 5072

South Asian (SAS) AF: 0.523 AC: 2413 AN: 4612

European-Finnish (FIN) AF: 0.347 AC: 3414 AN: 9840

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.390 AC: 26228 AN: 67222

Other (OTH) AF: 0.388 AC: 795 AN: 2050

Alfa AF: 0.212 Hom.: 476

Bravo AF: 0.359

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.10
DANN	Benign	0.16
PhyloP100		-3.8

Splicing

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

Other links and lift over

dbSNP: rs4568676; hg19: chr9-21184475; COSMIC: COSV70180333;