chr17-15368756-G-T

Variant names:

• chr17-15368756-G-T
• rs230884

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 0.286 in 151,886 control chromosomes in the GnomAD database, including 6,991 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 0.29 (6991 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0240
• Publications: 8 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 (AMR) allele frequency at 95% confidence interval = 0.419 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: 0.286 AC: 43398 AN: 151768 Hom.: 6988 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.286 AC: 43395 AN: 151886 Hom.: 6991 Cov.: 32 AF XY: 0.288 AC XY: 21343 AN XY: 74212

African (AFR) AF: 0.151 AC: 6238 AN: 41416

American (AMR) AF: 0.428 AC: 6523 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1267 AN: 3466

East Asian (EAS) AF: 0.276 AC: 1428 AN: 5174

South Asian (SAS) AF: 0.299 AC: 1441 AN: 4814

European-Finnish (FIN) AF: 0.304 AC: 3199 AN: 10538

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.326 AC: 22160 AN: 67916

Other (OTH) AF: 0.296 AC: 624 AN: 2108

Alfa AF: 0.317 Hom.: 34396

Bravo AF: 0.290

Asia WGS AF: 0.311 AC: 1083 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	0.95
DANN	Benign	0.45
PhyloP100		-0.024

Splicing

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

Other links and lift over

dbSNP: rs230884; hg19: chr17-15272073; COSMIC: COSV60076367;