17-15428200-T-G

Variant names:

• chr17-15428200-T-G
• rs2906966

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 0.136 in 152,192 control chromosomes in the GnomAD database, including 1,536 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 0.14 (1536 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0200
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20628 AN: 152074 Hom.: 1533 Cov.: 33

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.136 AC: 20637 AN: 152192 Hom.: 1536 Cov.: 33 AF XY: 0.136 AC XY: 10129 AN XY: 74422

African (AFR) AF: 0.131 AC: 5457 AN: 41510

American (AMR) AF: 0.134 AC: 2050 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 504 AN: 3472

East Asian (EAS) AF: 0.339 AC: 1755 AN: 5170

South Asian (SAS) AF: 0.109 AC: 527 AN: 4834

European-Finnish (FIN) AF: 0.126 AC: 1340 AN: 10596

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8597 AN: 67992

Other (OTH) AF: 0.137 AC: 289 AN: 2116

Alfa AF: 0.133 Hom.: 4615

Bravo AF: 0.137

Asia WGS AF: 0.199 AC: 695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.99
DANN	Benign	0.73
PhyloP100		-0.020

Splicing

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

Other links and lift over

dbSNP: rs2906966; hg19: chr17-15331517; COSMIC: COSV67896314;