15-66697894-T-G

Variant names:

• chr15-66697894-T-G
• rs2053424

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 0.317 in 152,162 control chromosomes in the GnomAD database, including 9,494 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 0.32 (9494 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.426 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: 0.317 AC: 48210 AN: 152044 Hom.: 9503 Cov.: 33

Gnomad AFR AF: 0.0823

Gnomad AMI AF: 0.606

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.317 AC: 48190 AN: 152162 Hom.: 9494 Cov.: 33 AF XY: 0.317 AC XY: 23613 AN XY: 74380

African (AFR) AF: 0.0821 AC: 3409 AN: 41544

American (AMR) AF: 0.266 AC: 4063 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1402 AN: 3470

East Asian (EAS) AF: 0.439 AC: 2269 AN: 5168

South Asian (SAS) AF: 0.310 AC: 1498 AN: 4830

European-Finnish (FIN) AF: 0.477 AC: 5043 AN: 10582

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.430 AC: 29257 AN: 67980

Other (OTH) AF: 0.301 AC: 635 AN: 2110

Alfa AF: 0.380 Hom.: 5856

Bravo AF: 0.292

Asia WGS AF: 0.360 AC: 1251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.19
DANN	Benign	0.62
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2053424; hg19: chr15-66990232;