chr7-15025359-G-A

Position:

• chr7-15025359-G-A

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 0.553 in 151,878 control chromosomes in the GnomAD database, including 23,599 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 (23599 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.101

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• 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	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.553 AC: 83993 AN: 151760 Hom.: 23586 Cov.: 31

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.554

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: 0.541

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

GnomAD4 genome AF: 0.553 AC: 84057 AN: 151878 Hom.: 23599 Cov.: 31 AF XY: 0.549 AC XY: 40722 AN XY: 74200

Gnomad4 AFR AF: 0.603

Gnomad4 AMR AF: 0.486

Gnomad4 ASJ AF: 0.554

Gnomad4 EAS AF: 0.680

Gnomad4 SAS AF: 0.622

Gnomad4 FIN AF: 0.439

Gnomad4 NFE AF: 0.543

Gnomad4 OTH AF: 0.547

Alfa AF: 0.538 Hom.: 20490

Bravo AF: 0.555

Asia WGS AF: 0.641 AC: 2227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6947830; hg19: chr7-15064984;