rs17367118

Variant names:

• chr2-122884035-G-A
• rs17367118
• ENST00000655733.1:n.2979-907G>A

Variant summary

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

The ENST00000655733.1(ENSG00000286481):​n.2979-907G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 152,054 control chromosomes in the GnomAD database, including 2,226 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 0.15 (2226 hom., cov: 32)
• Consequence: ENSG00000286481 ENST00000655733.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.695
• Publications: 13 publications found

Genes affected

ENSG00000286481 (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 (NFE) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373595	XR_923292.3	n.1308-907G>A		intron_variant	Intron 4 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286481	ENST00000655733.1	n.2979-907G>A		intron_variant	Intron 2 of 4
ENSG00000286481	ENST00000657880.2	n.1176-907G>A		intron_variant	Intron 6 of 8
ENSG00000286481	ENST00000687364.1	n.435-907G>A		intron_variant	Intron 3 of 5
ENSG00000286481	ENST00000770504.1	n.429-907G>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22773 AN: 151936 Hom.: 2226 Cov.: 32

Gnomad AFR AF: 0.0398

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.0810

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.0828

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.150 AC: 22776 AN: 152054 Hom.: 2226 Cov.: 32 AF XY: 0.146 AC XY: 10859 AN XY: 74322

African (AFR) AF: 0.0396 AC: 1645 AN: 41488

American (AMR) AF: 0.123 AC: 1882 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0810 AC: 281 AN: 3468

East Asian (EAS) AF: 0.105 AC: 542 AN: 5154

South Asian (SAS) AF: 0.0827 AC: 398 AN: 4812

European-Finnish (FIN) AF: 0.213 AC: 2248 AN: 10574

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.226 AC: 15359 AN: 67960

Other (OTH) AF: 0.135 AC: 284 AN: 2110

Alfa AF: 0.187 Hom.: 6109

Bravo AF: 0.138

Asia WGS AF: 0.112 AC: 389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.49
DANN	Benign	0.45
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs17367118; hg19: chr2-123641611;