rs17080239

Variant names:

• chr5-178177267-G-A
• rs17080239
• ENST00000697324.1:n.217-5613G>A

Variant summary

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

The ENST00000697324.1(ENSG00000289726):​n.217-5613G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 152,162 control chromosomes in the GnomAD database, including 3,464 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 0.20 (3464 hom., cov: 32)
• Consequence: ENSG00000289726 ENST00000697324.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 4 publications found

Genes affected

ENSG00000289726 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.261 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
ENSG00000289726	ENST00000697324.1	n.217-5613G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30772 AN: 152044 Hom.: 3459 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.202 AC: 30784 AN: 152162 Hom.: 3464 Cov.: 32 AF XY: 0.203 AC XY: 15104 AN XY: 74374

African (AFR) AF: 0.0998 AC: 4144 AN: 41526

American (AMR) AF: 0.211 AC: 3224 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 604 AN: 3472

East Asian (EAS) AF: 0.142 AC: 733 AN: 5174

South Asian (SAS) AF: 0.273 AC: 1316 AN: 4822

European-Finnish (FIN) AF: 0.276 AC: 2919 AN: 10576

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17291 AN: 67994

Other (OTH) AF: 0.172 AC: 363 AN: 2114

Alfa AF: 0.231 Hom.: 7958

Bravo AF: 0.190

Asia WGS AF: 0.202 AC: 703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.93
DANN	Benign	0.75
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs17080239; hg19: chr5-177604268;