chr15-91366093-C-T

Variant names:

• chr15-91366093-C-T
• rs5021331

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 0.221 in 152,016 control chromosomes in the GnomAD database, including 4,057 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 0.22 (4057 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.31 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: 0.221 AC: 33634 AN: 151898 Hom.: 4054 Cov.: 32

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.221 AC: 33659 AN: 152016 Hom.: 4057 Cov.: 32 AF XY: 0.217 AC XY: 16144 AN XY: 74314

African (AFR) AF: 0.303 AC: 12571 AN: 41440

American (AMR) AF: 0.198 AC: 3022 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 831 AN: 3466

East Asian (EAS) AF: 0.323 AC: 1669 AN: 5162

South Asian (SAS) AF: 0.131 AC: 631 AN: 4810

European-Finnish (FIN) AF: 0.146 AC: 1548 AN: 10596

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.187 AC: 12693 AN: 67950

Other (OTH) AF: 0.239 AC: 504 AN: 2112

Alfa AF: 0.215 Hom.: 700

Bravo AF: 0.230

Asia WGS AF: 0.234 AC: 816 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.57
DANN	Benign	0.52
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs5021331; hg19: chr15-91909323;