rs17526895

Positions:

• chr2-118058382-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0517 in 152,296 control chromosomes in the GnomAD database, including 273 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 0.052 (273 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.29

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0797 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0518 AC: 7881 AN: 152178 Hom.: 274 Cov.: 33

Gnomad AFR AF: 0.0128

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.0353

Gnomad ASJ AF: 0.0525

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0530

Gnomad FIN AF: 0.0610

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0815

Gnomad OTH AF: 0.0474

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

GnomAD4 genome AF: 0.0517 AC: 7874 AN: 152296 Hom.: 273 Cov.: 33 AF XY: 0.0500 AC XY: 3722 AN XY: 74468

Gnomad4 AFR AF: 0.0128

Gnomad4 AMR AF: 0.0352

Gnomad4 ASJ AF: 0.0525

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0529

Gnomad4 FIN AF: 0.0610

Gnomad4 NFE AF: 0.0815

Gnomad4 OTH AF: 0.0473

Alfa AF: 0.0731 Hom.: 565

Bravo AF: 0.0477

Asia WGS AF: 0.0240 AC: 83 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	17
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17526895; hg19: chr2-118815958;