17-13140986-T-C

Variant names:

• chr17-13140986-T-C
• rs9909179
• ENST00000835213.1:n.-208T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000835213.1(ENSG00000308590):​n.-208T>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 151,960 control chromosomes in the GnomAD database, including 10,645 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 0.37 (10645 hom., cov: 32)
• Consequence: ENSG00000308590 ENST00000835213.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.470
• Publications: 5 publications found

Genes affected

ENSG00000308590 (HGNC:):

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 (SAS) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000835213.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308590	ENST00000835213.1		n.-208T>C		upstream_gene	N/A
	ENSG00000308590	ENST00000835214.1		n.-227T>C		upstream_gene	N/A
	ENSG00000308590	ENST00000835215.1		n.-240T>C		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56188 AN: 151842 Hom.: 10632 Cov.: 32

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.370 AC: 56220 AN: 151960 Hom.: 10645 Cov.: 32 AF XY: 0.373 AC XY: 27702 AN XY: 74262

African (AFR) AF: 0.304 AC: 12584 AN: 41450

American (AMR) AF: 0.333 AC: 5096 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1044 AN: 3466

East Asian (EAS) AF: 0.374 AC: 1927 AN: 5152

South Asian (SAS) AF: 0.528 AC: 2541 AN: 4808

European-Finnish (FIN) AF: 0.412 AC: 4360 AN: 10570

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.405 AC: 27486 AN: 67912

Other (OTH) AF: 0.373 AC: 786 AN: 2110

Alfa AF: 0.388 Hom.: 38223

Bravo AF: 0.356

Asia WGS AF: 0.463 AC: 1606 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	7.6
DANN	Benign	0.46
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs9909179; hg19: chr17-13044303;