15-30003397-C-T

Variant names:

• chr15-30003397-C-T
• rs2140173

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 0.208 in 152,124 control chromosomes in the GnomAD database, including 3,683 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 0.21 (3683 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.368 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: 0.208 AC: 31651 AN: 152006 Hom.: 3683 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.208 AC: 31668 AN: 152124 Hom.: 3683 Cov.: 32 AF XY: 0.209 AC XY: 15508 AN XY: 74366

African (AFR) AF: 0.110 AC: 4548 AN: 41520

American (AMR) AF: 0.205 AC: 3141 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 908 AN: 3472

East Asian (EAS) AF: 0.382 AC: 1973 AN: 5162

South Asian (SAS) AF: 0.238 AC: 1144 AN: 4812

European-Finnish (FIN) AF: 0.226 AC: 2389 AN: 10574

Middle Eastern (MID) AF: 0.295 AC: 86 AN: 292

European-Non Finnish (NFE) AF: 0.246 AC: 16758 AN: 67984

Other (OTH) AF: 0.221 AC: 467 AN: 2112

Alfa AF: 0.236 Hom.: 7211

Bravo AF: 0.203

Asia WGS AF: 0.285 AC: 991 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.4
DANN	Benign	0.34
PhyloP100		0.013

Splicing

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

Other links and lift over

dbSNP: rs2140173; hg19: chr15-30295600;