rs17048681

Variant names:

• chr2-57138200-G-T
• rs17048681

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 0.578 in 151,920 control chromosomes in the GnomAD database, including 25,637 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 0.58 (25637 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.414

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.618 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: 0.578 AC: 87815 AN: 151804 Hom.: 25627 Cov.: 32

Gnomad AFR AF: 0.536

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.635

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.593

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

GnomAD4 genome AF: 0.578 AC: 87857 AN: 151920 Hom.: 25637 Cov.: 32 AF XY: 0.575 AC XY: 42706 AN XY: 74208

Gnomad4 AFR AF: 0.536

Gnomad4 AMR AF: 0.518

Gnomad4 ASJ AF: 0.635

Gnomad4 EAS AF: 0.372

Gnomad4 SAS AF: 0.584

Gnomad4 FIN AF: 0.616

Gnomad4 NFE AF: 0.623

Gnomad4 OTH AF: 0.595

Alfa AF: 0.609 Hom.: 57067

Bravo AF: 0.566

Asia WGS AF: 0.519 AC: 1806 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.35
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17048681; hg19: chr2-57365335;