7-15024591-A-T

Variant names:

• chr7-15024591-A-T
• rs10258074

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 151,958 control chromosomes in the GnomAD database, including 22,882 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 0.55 (22882 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.661 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: 0.545 AC: 82791 AN: 151842 Hom.: 22870 Cov.: 33

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.680

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.545 AC: 82852 AN: 151958 Hom.: 22882 Cov.: 33 AF XY: 0.541 AC XY: 40176 AN XY: 74238

African (AFR) AF: 0.574 AC: 23790 AN: 41442

American (AMR) AF: 0.483 AC: 7370 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.555 AC: 1927 AN: 3470

East Asian (EAS) AF: 0.680 AC: 3502 AN: 5148

South Asian (SAS) AF: 0.623 AC: 3000 AN: 4816

European-Finnish (FIN) AF: 0.439 AC: 4630 AN: 10544

Middle Eastern (MID) AF: 0.490 AC: 143 AN: 292

European-Non Finnish (NFE) AF: 0.543 AC: 36922 AN: 67968

Other (OTH) AF: 0.543 AC: 1148 AN: 2116

Alfa AF: 0.545 Hom.: 2805

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	-0.97
CADD	Benign	1.4
DANN	Benign	0.41
PhyloP100		-0.097

Splicing

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

Other links and lift over

dbSNP: rs10258074; hg19: chr7-15064216;