chr2-17089620-G-A

Variant names:

• chr2-17089620-G-A
• rs2013163

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 0.251 in 152,046 control chromosomes in the GnomAD database, including 6,179 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 0.25 (6179 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.353 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: 0.251 AC: 38195 AN: 151926 Hom.: 6183 Cov.: 31

Gnomad AFR AF: 0.0789

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.00810

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.251 AC: 38191 AN: 152046 Hom.: 6179 Cov.: 31 AF XY: 0.246 AC XY: 18293 AN XY: 74332

African (AFR) AF: 0.0787 AC: 3268 AN: 41538

American (AMR) AF: 0.273 AC: 4163 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.474 AC: 1644 AN: 3470

East Asian (EAS) AF: 0.00812 AC: 42 AN: 5170

South Asian (SAS) AF: 0.244 AC: 1178 AN: 4818

European-Finnish (FIN) AF: 0.249 AC: 2623 AN: 10554

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.357 AC: 24212 AN: 67912

Other (OTH) AF: 0.286 AC: 605 AN: 2112

Alfa AF: 0.295 Hom.: 986

Bravo AF: 0.244

Asia WGS AF: 0.116 AC: 406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.39
DANN	Benign	0.62
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2013163; hg19: chr2-17270887;