rs17048681

Variant names:

• chr2-57138200-G-T
• rs17048681

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.536 AC: 22183 AN: 41420

American (AMR) AF: 0.518 AC: 7918 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.635 AC: 2203 AN: 3468

East Asian (EAS) AF: 0.372 AC: 1918 AN: 5156

South Asian (SAS) AF: 0.584 AC: 2817 AN: 4822

European-Finnish (FIN) AF: 0.616 AC: 6486 AN: 10526

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.623 AC: 42356 AN: 67948

Other (OTH) AF: 0.595 AC: 1249 AN: 2098

Alfa AF: 0.604 Hom.: 86746

Bravo AF: 0.566

Asia WGS AF: 0.519 AC: 1806 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.35
DANN	Benign	0.57
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs17048681; hg19: chr2-57365335;