chr15-101157777-T-C

Variant names:

• chr15-101157777-T-C
• rs1809180

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 0.877 in 152,260 control chromosomes in the GnomAD database, including 58,756 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 0.88 (58756 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.933
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.877 AC: 133382 AN: 152142 Hom.: 58722 Cov.: 34

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.826

Gnomad AMR AF: 0.912

Gnomad ASJ AF: 0.909

Gnomad EAS AF: 0.816

Gnomad SAS AF: 0.907

Gnomad FIN AF: 0.911

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.909

Gnomad OTH AF: 0.887

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

GnomAD4 genome AF: 0.877 AC: 133472 AN: 152260 Hom.: 58756 Cov.: 34 AF XY: 0.878 AC XY: 65339 AN XY: 74444

African (AFR) AF: 0.804 AC: 33398 AN: 41548

American (AMR) AF: 0.912 AC: 13954 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.909 AC: 3155 AN: 3472

East Asian (EAS) AF: 0.816 AC: 4211 AN: 5160

South Asian (SAS) AF: 0.908 AC: 4375 AN: 4818

European-Finnish (FIN) AF: 0.911 AC: 9676 AN: 10618

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.909 AC: 61829 AN: 68018

Other (OTH) AF: 0.882 AC: 1865 AN: 2114

Alfa AF: 0.901 Hom.: 120320

Bravo AF: 0.871

Asia WGS AF: 0.876 AC: 3050 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.1
DANN	Benign	0.80
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs1809180; hg19: chr15-101697982;