rs17587352

Variant names:

• chr2-118085861-T-C
• rs17587352
• ENST00000747789.1:n.231+1652A>G

Variant summary

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

The ENST00000747789.1(ENSG00000297418):​n.231+1652A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0707 in 152,236 control chromosomes in the GnomAD database, including 531 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 0.071 (531 hom., cov: 33)
• Consequence: ENSG00000297418 ENST00000747789.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.326
• Publications: 5 publications found

Genes affected

ENSG00000297418 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.1 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985940	XR_001739662.3	n.181+2390A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297418	ENST00000747789.1	n.231+1652A>G		intron_variant	Intron 2 of 4
ENSG00000297418	ENST00000747790.1	n.104+2390A>G		intron_variant	Intron 1 of 2
ENSG00000297418	ENST00000747791.1	n.271+1652A>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.0706 AC: 10738 AN: 152118 Hom.: 527 Cov.: 33

Gnomad AFR AF: 0.0263

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0655

Gnomad EAS AF: 0.0408

Gnomad SAS AF: 0.0637

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0750

Gnomad OTH AF: 0.0621

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

GnomAD4 genome AF: 0.0707 AC: 10760 AN: 152236 Hom.: 531 Cov.: 33 AF XY: 0.0762 AC XY: 5670 AN XY: 74412

African (AFR) AF: 0.0263 AC: 1091 AN: 41554

American (AMR) AF: 0.105 AC: 1600 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0655 AC: 227 AN: 3468

East Asian (EAS) AF: 0.0407 AC: 211 AN: 5186

South Asian (SAS) AF: 0.0637 AC: 307 AN: 4818

European-Finnish (FIN) AF: 0.183 AC: 1941 AN: 10592

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0750 AC: 5102 AN: 68008

Other (OTH) AF: 0.0681 AC: 144 AN: 2114

Alfa AF: 0.0706 Hom.: 711

Bravo AF: 0.0631

Asia WGS AF: 0.0640 AC: 222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	11
DANN	Benign	0.82
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs17587352; hg19: chr2-118843437; COSMIC: COSV55522177;