rs2089114

Variant names:

• chr17-42625233-C-T
• rs2089114
• ENST00000766603.1:n.31-5909G>A

Variant summary

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

The ENST00000766603.1(ENSG00000299802):​n.31-5909G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 151,868 control chromosomes in the GnomAD database, including 21,084 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 0.53 (21084 hom., cov: 30)
• Consequence: ENSG00000299802 ENST00000766603.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.250
• Publications: 15 publications found

Genes affected

ENSG00000299802 (HGNC:):

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 (SAS) allele frequency at 95% confidence interval = 0.627 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
ENSG00000299802	ENST00000766603.1	n.31-5909G>A		intron_variant	Intron 1 of 3
ENSG00000299802	ENST00000766604.1	n.117-5909G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.525 AC: 79740 AN: 151750 Hom.: 21048 Cov.: 30

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.526 AC: 79826 AN: 151868 Hom.: 21084 Cov.: 30 AF XY: 0.523 AC XY: 38798 AN XY: 74188

African (AFR) AF: 0.512 AC: 21194 AN: 41406

American (AMR) AF: 0.483 AC: 7365 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1354 AN: 3472

East Asian (EAS) AF: 0.459 AC: 2355 AN: 5132

South Asian (SAS) AF: 0.646 AC: 3109 AN: 4816

European-Finnish (FIN) AF: 0.530 AC: 5584 AN: 10532

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.549 AC: 37278 AN: 67948

Other (OTH) AF: 0.495 AC: 1046 AN: 2112

Alfa AF: 0.544 Hom.: 11786

Bravo AF: 0.516

Asia WGS AF: 0.597 AC: 2077 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	3.6
DANN	Benign	0.91
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs2089114; hg19: chr17-40777251;