rs2052011

chr17-13396246-C-G

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 0.903 in 152,316 control chromosomes in the GnomAD database, including 62,335 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 0.90 (62335 hom., cov: 35)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.903 AC: 137438 AN: 152198 Hom.: 62298 Cov.: 35

Gnomad AFR AF: 0.827

Gnomad AMI AF: 0.865

Gnomad AMR AF: 0.942

Gnomad ASJ AF: 0.940

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.928

Gnomad FIN AF: 0.914

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.928

Gnomad OTH AF: 0.905

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

GnomAD4 genome AF: 0.903 AC: 137530 AN: 152316 Hom.: 62335 Cov.: 35 AF XY: 0.904 AC XY: 67347 AN XY: 74478

Gnomad4 AFR AF: 0.827

Gnomad4 AMR AF: 0.943

Gnomad4 ASJ AF: 0.940

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.927

Gnomad4 FIN AF: 0.914

Gnomad4 NFE AF: 0.928

Gnomad4 OTH AF: 0.906

Alfa AF: 0.919 Hom.: 8001

Bravo AF: 0.904

Asia WGS AF: 0.952 AC: 3310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.057
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2052011; hg19: chr17-13299563;