9-12443586-A-G

Variant names:

• chr9-12443586-A-G
• rs7860071

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 0.716 in 151,882 control chromosomes in the GnomAD database, including 39,104 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 0.72 (39104 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.196
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.749 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: 0.716 AC: 108679 AN: 151764 Hom.: 39063 Cov.: 32

Gnomad AFR AF: 0.756

Gnomad AMI AF: 0.776

Gnomad AMR AF: 0.735

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.735

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.716 AC: 108773 AN: 151882 Hom.: 39104 Cov.: 32 AF XY: 0.717 AC XY: 53197 AN XY: 74230

African (AFR) AF: 0.756 AC: 31363 AN: 41476

American (AMR) AF: 0.735 AC: 11189 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.621 AC: 2152 AN: 3464

East Asian (EAS) AF: 0.744 AC: 3842 AN: 5166

South Asian (SAS) AF: 0.664 AC: 3201 AN: 4818

European-Finnish (FIN) AF: 0.735 AC: 7779 AN: 10578

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.691 AC: 46864 AN: 67834

Other (OTH) AF: 0.704 AC: 1483 AN: 2108

Alfa AF: 0.695 Hom.: 157424

Bravo AF: 0.720

Asia WGS AF: 0.664 AC: 2305 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.82
DANN	Benign	0.58
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs7860071; hg19: chr9-12443586;