7-15024630-G-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.574

Gnomad4 AMR AF: 0.484

Gnomad4 ASJ AF: 0.555

Gnomad4 EAS AF: 0.680

Gnomad4 SAS AF: 0.622

Gnomad4 FIN AF: 0.440

Gnomad4 NFE AF: 0.543

Gnomad4 OTH AF: 0.542

Alfa AF: 0.552 Hom.: 10701

Bravo AF: 0.546

Asia WGS AF: 0.641 AC: 2226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.2
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2191348; hg19: chr7-15064255;