rs17385675

Positions:

• chr2-201942473-C-T

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 0.0613 in 152,146 control chromosomes in the GnomAD database, including 342 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 0.061 (342 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0802 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.201942473C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0614 AC: 9332 AN: 152028 Hom.: 343 Cov.: 31

Gnomad AFR AF: 0.0282

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.0753

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.0226

Gnomad FIN AF: 0.0486

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0820

Gnomad OTH AF: 0.0793

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

GnomAD4 genome AF: 0.0613 AC: 9325 AN: 152146 Hom.: 342 Cov.: 31 AF XY: 0.0595 AC XY: 4429 AN XY: 74388

Gnomad4 AFR AF: 0.0282

Gnomad4 AMR AF: 0.0752

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.00271

Gnomad4 SAS AF: 0.0226

Gnomad4 FIN AF: 0.0486

Gnomad4 NFE AF: 0.0820

Gnomad4 OTH AF: 0.0781

Alfa AF: 0.0799 Hom.: 956

Bravo AF: 0.0625

Asia WGS AF: 0.0170 AC: 61 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.0080
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: rs17385675; hg19: chr2-202807196;