rs17042998

Variant names:

• chr2-113141948-A-G
• rs17042998

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 0.0413 in 152,264 control chromosomes in the GnomAD database, including 848 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 0.041 (848 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0413 AC: 6279 AN: 152146 Hom.: 847 Cov.: 32

Gnomad AFR AF: 0.00736

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0545

Gnomad ASJ AF: 0.00836

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.0691

Gnomad FIN AF: 0.0609

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0184

Gnomad OTH AF: 0.0363

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

GnomAD4 genome AF: 0.0413 AC: 6281 AN: 152264 Hom.: 848 Cov.: 32 AF XY: 0.0471 AC XY: 3503 AN XY: 74436

Gnomad4 AFR AF: 0.00734

Gnomad4 AMR AF: 0.0552

Gnomad4 ASJ AF: 0.00836

Gnomad4 EAS AF: 0.538

Gnomad4 SAS AF: 0.0679

Gnomad4 FIN AF: 0.0609

Gnomad4 NFE AF: 0.0184

Gnomad4 OTH AF: 0.0369

Alfa AF: 0.0297 Hom.: 99

Bravo AF: 0.0448

Asia WGS AF: 0.248 AC: 863 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.0
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17042998; hg19: chr2-113899525;