rs2137476

Variant names:

• chr17-53103164-C-T
• rs2137476

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 0.7 in 151,996 control chromosomes in the GnomAD database, including 41,819 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 0.70 (41819 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.853 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: 0.701 AC: 106422 AN: 151878 Hom.: 41809 Cov.: 31

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.916

Gnomad AMR AF: 0.821

Gnomad ASJ AF: 0.853

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.877

Gnomad MID AF: 0.787

Gnomad NFE AF: 0.859

Gnomad OTH AF: 0.752

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

GnomAD4 genome AF: 0.700 AC: 106447 AN: 151996 Hom.: 41819 Cov.: 31 AF XY: 0.705 AC XY: 52376 AN XY: 74272

Gnomad4 AFR AF: 0.307

Gnomad4 AMR AF: 0.821

Gnomad4 ASJ AF: 0.853

Gnomad4 EAS AF: 0.744

Gnomad4 SAS AF: 0.844

Gnomad4 FIN AF: 0.877

Gnomad4 NFE AF: 0.859

Gnomad4 OTH AF: 0.749

Alfa AF: 0.800 Hom.: 15651

Bravo AF: 0.678

Asia WGS AF: 0.766 AC: 2660 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.10
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2137476; hg19: chr17-51180525;