rs7169431

Positions:

• chr15-56048698-A-G
• chr15-56048698-A-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 0.875 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.770

Gnomad4 AMR AF: 0.914

Gnomad4 ASJ AF: 0.862

Gnomad4 EAS AF: 0.871

Gnomad4 SAS AF: 0.929

Gnomad4 FIN AF: 0.944

Gnomad4 NFE AF: 0.916

Gnomad4 OTH AF: 0.868

Alfa AF: 0.908 Hom.: 122113

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7169431; hg19: chr15-56340896;