chr17-15396028-A-G

Position:

• chr17-15396028-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.935 in 152,050 control chromosomes in the GnomAD database, including 66,737 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 0.94 (66737 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.969 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.15396028A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000266667	ENST00000580422.1	n.315-13907T>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.936 AC: 142138 AN: 151932 Hom.: 66696 Cov.: 30

Gnomad AFR AF: 0.861

Gnomad AMI AF: 0.963

Gnomad AMR AF: 0.954

Gnomad ASJ AF: 0.933

Gnomad EAS AF: 0.905

Gnomad SAS AF: 0.901

Gnomad FIN AF: 0.973

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.975

Gnomad OTH AF: 0.941

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

GnomAD4 genome AF: 0.935 AC: 142235 AN: 152050 Hom.: 66737 Cov.: 30 AF XY: 0.935 AC XY: 69497 AN XY: 74316

Gnomad4 AFR AF: 0.860

Gnomad4 AMR AF: 0.954

Gnomad4 ASJ AF: 0.933

Gnomad4 EAS AF: 0.906

Gnomad4 SAS AF: 0.900

Gnomad4 FIN AF: 0.973

Gnomad4 NFE AF: 0.975

Gnomad4 OTH AF: 0.942

Alfa AF: 0.964 Hom.: 59029

Bravo AF: 0.930

Asia WGS AF: 0.897 AC: 3121 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.2
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2024158; hg19: chr17-15299345;