7-15024684-G-T

Variant names:

• chr7-15024684-G-T
• rs2191349

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 0.545 in 151,844 control chromosomes in the GnomAD database, including 22,800 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 0.54 (22800 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 178 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.662 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: 0.545 AC: 82623 AN: 151724 Hom.: 22786 Cov.: 32

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.681

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.545 AC: 82687 AN: 151844 Hom.: 22800 Cov.: 32 AF XY: 0.541 AC XY: 40116 AN XY: 74204

African (AFR) AF: 0.573 AC: 23737 AN: 41390

American (AMR) AF: 0.483 AC: 7362 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.554 AC: 1923 AN: 3468

East Asian (EAS) AF: 0.681 AC: 3495 AN: 5130

South Asian (SAS) AF: 0.622 AC: 2997 AN: 4816

European-Finnish (FIN) AF: 0.439 AC: 4632 AN: 10548

Middle Eastern (MID) AF: 0.497 AC: 145 AN: 292

European-Non Finnish (NFE) AF: 0.542 AC: 36839 AN: 67948

Other (OTH) AF: 0.540 AC: 1136 AN: 2104

Alfa AF: 0.546 Hom.: 86011

Bravo AF: 0.546

Asia WGS AF: 0.641 AC: 2226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.7
DANN	Benign	0.74
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs2191349; hg19: chr7-15064309;