rs7169431

Variant names:

• chr15-56048698-A-G
• rs7169431

Your query was ambiguous. Multiple possible variants found:

• chr15-56048698-A-G
• chr15-56048698-A-T

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 0.875 in 152,056 control chromosomes in the GnomAD database, including 58,494 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 0.87 (58494 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.500
• Publications: 26 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.91 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.875 AC: 132922 AN: 151938 Hom.: 58445 Cov.: 31

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.914

Gnomad AMR AF: 0.914

Gnomad ASJ AF: 0.862

Gnomad EAS AF: 0.871

Gnomad SAS AF: 0.929

Gnomad FIN AF: 0.944

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.916

Gnomad OTH AF: 0.867

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

GnomAD4 genome AF: 0.875 AC: 133029 AN: 152056 Hom.: 58494 Cov.: 31 AF XY: 0.879 AC XY: 65317 AN XY: 74342

African (AFR) AF: 0.770 AC: 31916 AN: 41440

American (AMR) AF: 0.914 AC: 13974 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.862 AC: 2992 AN: 3472

East Asian (EAS) AF: 0.871 AC: 4478 AN: 5140

South Asian (SAS) AF: 0.929 AC: 4472 AN: 4812

European-Finnish (FIN) AF: 0.944 AC: 10006 AN: 10596

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.916 AC: 62271 AN: 67988

Other (OTH) AF: 0.868 AC: 1834 AN: 2114

Alfa AF: 0.900 Hom.: 188277

Bravo AF: 0.867

Asia WGS AF: 0.906 AC: 3149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.11
DANN	Benign	0.38
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs7169431; hg19: chr15-56340896;