9-21076687-G-C

Variant names:

• chr9-21076687-G-C
• rs1364612

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 0.131 in 147,866 control chromosomes in the GnomAD database, including 1,324 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 0.13 (1324 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52
• Publications: 6 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 = 0.189 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19362 AN: 147752 Hom.: 1322 Cov.: 31

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.108

Gnomad AMR AF: 0.0879

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.0570

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.131 AC: 19366 AN: 147866 Hom.: 1324 Cov.: 31 AF XY: 0.129 AC XY: 9308 AN XY: 72228

African (AFR) AF: 0.154 AC: 6328 AN: 41182

American (AMR) AF: 0.0878 AC: 1301 AN: 14818

Ashkenazi Jewish (ASJ) AF: 0.222 AC: 729 AN: 3288

East Asian (EAS) AF: 0.199 AC: 1028 AN: 5172

South Asian (SAS) AF: 0.179 AC: 826 AN: 4608

European-Finnish (FIN) AF: 0.0570 AC: 580 AN: 10174

Middle Eastern (MID) AF: 0.241 AC: 68 AN: 282

European-Non Finnish (NFE) AF: 0.124 AC: 8119 AN: 65438

Other (OTH) AF: 0.144 AC: 292 AN: 2026

Alfa AF: 0.0468 Hom.: 37

Bravo AF: 0.131

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.13
DANN	Benign	0.42
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1364612; hg19: chr9-21076686; COSMIC: COSV66525670;