7-96748728-G-A

Variant names:

• chr7-96748728-G-A
• rs12673393

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 0.0823 in 152,238 control chromosomes in the GnomAD database, including 599 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 0.082 (599 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.350
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.127 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: 0.0823 AC: 12527 AN: 152120 Hom.: 597 Cov.: 33

Gnomad AFR AF: 0.0397

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.0741

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.0799

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.0823 AC: 12528 AN: 152238 Hom.: 599 Cov.: 33 AF XY: 0.0827 AC XY: 6158 AN XY: 74442

African (AFR) AF: 0.0400 AC: 1660 AN: 41538

American (AMR) AF: 0.0739 AC: 1130 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 514 AN: 3472

East Asian (EAS) AF: 0.101 AC: 520 AN: 5170

South Asian (SAS) AF: 0.136 AC: 655 AN: 4826

European-Finnish (FIN) AF: 0.0799 AC: 846 AN: 10592

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6872 AN: 68022

Other (OTH) AF: 0.104 AC: 220 AN: 2114

Alfa AF: 0.0980 Hom.: 480

Bravo AF: 0.0802

Asia WGS AF: 0.107 AC: 374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.1
DANN	Benign	0.23
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs12673393; hg19: chr7-96378040;