rs2020932

Variant names:

• chr17-30236481-T-A
• rs2020932

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 0.131 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.347 AC: 14287 AN: 41150

American (AMR) AF: 0.0720 AC: 1098 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.0934 AC: 324 AN: 3468

East Asian (EAS) AF: 0.0501 AC: 257 AN: 5130

South Asian (SAS) AF: 0.100 AC: 482 AN: 4804

European-Finnish (FIN) AF: 0.0246 AC: 259 AN: 10548

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0418 AC: 2839 AN: 67972

Other (OTH) AF: 0.115 AC: 242 AN: 2104

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
PhyloP100		-0.14
PromoterAI		-0.0018	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2020932; hg19: chr17-28563499;