chr7-15024630-G-T

Variant names:

• chr7-15024630-G-T
• rs2191348

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 151,948 control chromosomes in the GnomAD database, including 22,876 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 (22876 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.126
• Publications: 28 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• 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
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: 0.545 AC: 82787 AN: 151828 Hom.: 22864 Cov.: 32

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.460

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.680

Gnomad SAS AF: 0.621

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.510

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: 82848 AN: 151948 Hom.: 22876 Cov.: 32 AF XY: 0.541 AC XY: 40190 AN XY: 74240

African (AFR) AF: 0.574 AC: 23782 AN: 41448

American (AMR) AF: 0.484 AC: 7375 AN: 15252

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

East Asian (EAS) AF: 0.680 AC: 3497 AN: 5142

South Asian (SAS) AF: 0.622 AC: 2992 AN: 4810

European-Finnish (FIN) AF: 0.440 AC: 4642 AN: 10542

Middle Eastern (MID) AF: 0.493 AC: 143 AN: 290

European-Non Finnish (NFE) AF: 0.543 AC: 36929 AN: 67978

Other (OTH) AF: 0.542 AC: 1143 AN: 2108

Alfa AF: 0.555 Hom.: 14384

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	-0.91
CADD	Benign	2.2
DANN	Benign	0.36
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs2191348; hg19: chr7-15064255;