rs17587100

Positions:

• chr2-118080834-A-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 0.0683 in 152,258 control chromosomes in the GnomAD database, including 509 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 0.068 (509 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.560

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.118080834A>C		intergenic_region
LOC107985940	XR_001739662.3	n.181+7417T>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0681 AC: 10363 AN: 152140 Hom.: 504 Cov.: 32

Gnomad AFR AF: 0.0224

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.0606

Gnomad EAS AF: 0.0406

Gnomad SAS AF: 0.0661

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0731

Gnomad OTH AF: 0.0602

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

GnomAD4 genome AF: 0.0683 AC: 10396 AN: 152258 Hom.: 509 Cov.: 32 AF XY: 0.0740 AC XY: 5512 AN XY: 74440

Gnomad4 AFR AF: 0.0226

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.0606

Gnomad4 EAS AF: 0.0403

Gnomad4 SAS AF: 0.0663

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.0732

Gnomad4 OTH AF: 0.0667

Alfa AF: 0.0696 Hom.: 59

Bravo AF: 0.0612

Asia WGS AF: 0.0660 AC: 231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.7
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17587100; hg19: chr2-118838410; COSMIC: COSV60100147;