rs2020932

Positions:

• chr17-30236481-T-A

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 0.131 in 151,626 control chromosomes in the GnomAD database, including 2,729 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 0.13 (2729 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.138

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.342 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: 0.130 AC: 19764 AN: 151510 Hom.: 2713 Cov.: 31

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0723

Gnomad ASJ AF: 0.0934

Gnomad EAS AF: 0.0510

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0246

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0418

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.131 AC: 19818 AN: 151626 Hom.: 2729 Cov.: 31 AF XY: 0.129 AC XY: 9537 AN XY: 74096

Gnomad4 AFR AF: 0.347

Gnomad4 AMR AF: 0.0720

Gnomad4 ASJ AF: 0.0934

Gnomad4 EAS AF: 0.0501

Gnomad4 SAS AF: 0.100

Gnomad4 FIN AF: 0.0246

Gnomad4 NFE AF: 0.0418

Gnomad4 OTH AF: 0.115

Alfa AF: 0.0933 Hom.: 207

Bravo AF: 0.142

Asia WGS AF: 0.0950 AC: 331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2020932; hg19: chr17-28563499;