2-116580208-A-G

Variant names:

• chr2-116580208-A-G
• rs2920164

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 0.252 in 152,182 control chromosomes in the GnomAD database, including 5,175 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 (5175 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.276
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.431 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: 0.252 AC: 38346 AN: 152066 Hom.: 5174 Cov.: 33

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.252 AC: 38365 AN: 152182 Hom.: 5175 Cov.: 33 AF XY: 0.253 AC XY: 18814 AN XY: 74400

African (AFR) AF: 0.180 AC: 7461 AN: 41520

American (AMR) AF: 0.203 AC: 3101 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1002 AN: 3468

East Asian (EAS) AF: 0.446 AC: 2305 AN: 5172

South Asian (SAS) AF: 0.194 AC: 938 AN: 4828

European-Finnish (FIN) AF: 0.325 AC: 3441 AN: 10588

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.284 AC: 19312 AN: 67990

Other (OTH) AF: 0.269 AC: 568 AN: 2114

Alfa AF: 0.257 Hom.: 920

Bravo AF: 0.240

Asia WGS AF: 0.256 AC: 889 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.0
DANN	Benign	0.53
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs2920164; hg19: chr2-117337784;