17-5739998-C-T

Variant names:

• chr17-5739998-C-T
• rs8080616
• ENST00000783338.1:n.186+32672G>A

Variant summary

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

The ENST00000783338.1(ENSG00000286356):​n.186+32672G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 144,436 control chromosomes in the GnomAD database, including 16,378 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 0.48 (16378 hom., cov: 27)
• Consequence: ENSG00000286356 ENST00000783338.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 1 publications found

Genes affected

ENSG00000286356 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.519 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
ENSG00000286356	ENST00000783338.1	n.186+32672G>A		intron_variant	Intron 1 of 1
ENSG00000286356	ENST00000783339.1	n.174-20653G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.480 AC: 69345 AN: 144364 Hom.: 16363 Cov.: 27

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.481 AC: 69404 AN: 144436 Hom.: 16378 Cov.: 27 AF XY: 0.478 AC XY: 33424 AN XY: 69938

African (AFR) AF: 0.517 AC: 20042 AN: 38796

American (AMR) AF: 0.529 AC: 7738 AN: 14628

Ashkenazi Jewish (ASJ) AF: 0.531 AC: 1810 AN: 3408

East Asian (EAS) AF: 0.292 AC: 1381 AN: 4730

South Asian (SAS) AF: 0.419 AC: 1892 AN: 4518

European-Finnish (FIN) AF: 0.427 AC: 3740 AN: 8756

Middle Eastern (MID) AF: 0.428 AC: 119 AN: 278

European-Non Finnish (NFE) AF: 0.472 AC: 31317 AN: 66406

Other (OTH) AF: 0.492 AC: 1003 AN: 2040

Alfa AF: 0.292 Hom.: 634

Bravo AF: 0.481

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.61
DANN	Benign	0.46
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs8080616; hg19: chr17-5643318;