7-80230790-A-G

Variant names:

• chr7-80230790-A-G
• rs12706724

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 0.603 in 152,034 control chromosomes in the GnomAD database, including 31,707 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 0.60 (31707 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.696
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.849 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91603 AN: 151916 Hom.: 31692 Cov.: 31

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.735

Gnomad AMR AF: 0.727

Gnomad ASJ AF: 0.758

Gnomad EAS AF: 0.870

Gnomad SAS AF: 0.836

Gnomad FIN AF: 0.749

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.729

Gnomad OTH AF: 0.659

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

GnomAD4 genome AF: 0.603 AC: 91640 AN: 152034 Hom.: 31707 Cov.: 31 AF XY: 0.612 AC XY: 45490 AN XY: 74310

African (AFR) AF: 0.233 AC: 9664 AN: 41468

American (AMR) AF: 0.727 AC: 11102 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.758 AC: 2629 AN: 3470

East Asian (EAS) AF: 0.871 AC: 4491 AN: 5158

South Asian (SAS) AF: 0.836 AC: 4030 AN: 4820

European-Finnish (FIN) AF: 0.749 AC: 7916 AN: 10566

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.729 AC: 49537 AN: 67966

Other (OTH) AF: 0.663 AC: 1399 AN: 2110

Alfa AF: 0.699 Hom.: 16347

Bravo AF: 0.585

Asia WGS AF: 0.834 AC: 2900 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.36
DANN	Benign	0.35
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs12706724; hg19: chr7-79860106;