chr7-96447615-G-A

Variant names:

• chr7-96447615-G-A
• rs2724041

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.642 in 152,006 control chromosomes in the GnomAD database, including 32,207 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 0.64 (32207 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.67
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.851 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: 0.642 AC: 97457 AN: 151888 Hom.: 32159 Cov.: 32

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.873

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.642 AC: 97562 AN: 152006 Hom.: 32207 Cov.: 32 AF XY: 0.642 AC XY: 47715 AN XY: 74282

African (AFR) AF: 0.776 AC: 32159 AN: 41468

American (AMR) AF: 0.655 AC: 10007 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.648 AC: 2246 AN: 3466

East Asian (EAS) AF: 0.873 AC: 4511 AN: 5170

South Asian (SAS) AF: 0.601 AC: 2892 AN: 4808

European-Finnish (FIN) AF: 0.546 AC: 5758 AN: 10552

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.555 AC: 37709 AN: 67944

Other (OTH) AF: 0.680 AC: 1438 AN: 2116

Alfa AF: 0.587 Hom.: 118609

Bravo AF: 0.660

Asia WGS AF: 0.774 AC: 2689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	18
DANN	Benign	0.60
PhyloP100		2.7

Splicing

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

Other links and lift over

dbSNP: rs2724041; hg19: chr7-96076927;