7-15024684-G-T

Position:

• chr7-15024684-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 151,844 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

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

Gnomad4 AFR AF: 0.573

Gnomad4 AMR AF: 0.483

Gnomad4 ASJ AF: 0.554

Gnomad4 EAS AF: 0.681

Gnomad4 SAS AF: 0.622

Gnomad4 FIN AF: 0.439

Gnomad4 NFE AF: 0.542

Gnomad4 OTH AF: 0.540

Alfa AF: 0.545 Hom.: 34360

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	-0.85
CADD	Benign	4.7
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2191349; hg19: chr7-15064309;