rs17587352

Positions:

• chr2-118085861-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.326

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.118085861T>C		intergenic_region
LOC107985940	XR_001739662.3	n.181+2390A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.0263

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.0655

Gnomad4 EAS AF: 0.0407

Gnomad4 SAS AF: 0.0637

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.0750

Gnomad4 OTH AF: 0.0681

Alfa AF: 0.0714 Hom.: 568

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

Splicing

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

Publications

LitVar

Other links and lift over

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