rs2137476

Positions:

• chr17-53103164-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;