9-85303316-G-A

Variant names:

• chr9-85303316-G-A
• rs2769595

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 0.439 in 152,080 control chromosomes in the GnomAD database, including 16,675 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 0.44 (16675 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.587
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.561 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.440 AC: 66792 AN: 151962 Hom.: 16682 Cov.: 32

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.439 AC: 66793 AN: 152080 Hom.: 16675 Cov.: 32 AF XY: 0.439 AC XY: 32661 AN XY: 74324

African (AFR) AF: 0.215 AC: 8930 AN: 41488

American (AMR) AF: 0.423 AC: 6469 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.536 AC: 1862 AN: 3472

East Asian (EAS) AF: 0.195 AC: 1005 AN: 5164

South Asian (SAS) AF: 0.579 AC: 2785 AN: 4814

European-Finnish (FIN) AF: 0.538 AC: 5673 AN: 10546

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.565 AC: 38392 AN: 67990

Other (OTH) AF: 0.475 AC: 1004 AN: 2112

Alfa AF: 0.368 Hom.: 1533

Bravo AF: 0.414

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.30
DANN	Benign	0.52
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs2769595; hg19: chr9-87918231;