chr7-15025359-G-A

Variant names:

• chr7-15025359-G-A
• rs6947830

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 0.553 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
• Publications: 23 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.553 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

African (AFR) AF: 0.603 AC: 24969 AN: 41404

American (AMR) AF: 0.486 AC: 7415 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.554 AC: 1924 AN: 3470

East Asian (EAS) AF: 0.680 AC: 3493 AN: 5140

South Asian (SAS) AF: 0.622 AC: 2992 AN: 4808

European-Finnish (FIN) AF: 0.439 AC: 4630 AN: 10540

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.543 AC: 36915 AN: 67932

Other (OTH) AF: 0.547 AC: 1153 AN: 2108

Alfa AF: 0.549 Hom.: 71991

Bravo AF: 0.555

Asia WGS AF: 0.641 AC: 2227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.31
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs6947830; hg19: chr7-15064984;