15-94691904-G-T

Variant names:

• chr15-94691904-G-T
• rs2199724

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 0.595 in 152,004 control chromosomes in the GnomAD database, including 28,068 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 0.59 (28068 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.348
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.777 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.594 AC: 90279 AN: 151886 Hom.: 28016 Cov.: 32

Gnomad AFR AF: 0.784

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.565

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.562

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

GnomAD4 genome AF: 0.595 AC: 90390 AN: 152004 Hom.: 28068 Cov.: 32 AF XY: 0.594 AC XY: 44116 AN XY: 74298

African (AFR) AF: 0.784 AC: 32518 AN: 41480

American (AMR) AF: 0.485 AC: 7408 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.579 AC: 2008 AN: 3468

East Asian (EAS) AF: 0.446 AC: 2302 AN: 5164

South Asian (SAS) AF: 0.575 AC: 2777 AN: 4826

European-Finnish (FIN) AF: 0.565 AC: 5955 AN: 10548

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.526 AC: 35744 AN: 67940

Other (OTH) AF: 0.563 AC: 1186 AN: 2106

Alfa AF: 0.556 Hom.: 45228

Bravo AF: 0.594

Asia WGS AF: 0.551 AC: 1917 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.24
DANN	Benign	0.42
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs2199724; hg19: chr15-95235133;