2-180396890-A-G

Variant names:

• chr2-180396890-A-G
• rs2176588

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 0.39 in 144,882 control chromosomes in the GnomAD database, including 12,365 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 0.39 (12365 hom., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.542
• Publications: 2 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 (NFE) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.390 AC: 56474 AN: 144816 Hom.: 12370 Cov.: 24

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.390 AC: 56446 AN: 144882 Hom.: 12365 Cov.: 24 AF XY: 0.382 AC XY: 26833 AN XY: 70192

African (AFR) AF: 0.215 AC: 8627 AN: 40058

American (AMR) AF: 0.369 AC: 5348 AN: 14482

Ashkenazi Jewish (ASJ) AF: 0.563 AC: 1928 AN: 3422

East Asian (EAS) AF: 0.397 AC: 1919 AN: 4830

South Asian (SAS) AF: 0.317 AC: 1482 AN: 4674

European-Finnish (FIN) AF: 0.390 AC: 3224 AN: 8270

Middle Eastern (MID) AF: 0.574 AC: 155 AN: 270

European-Non Finnish (NFE) AF: 0.492 AC: 32501 AN: 66032

Other (OTH) AF: 0.432 AC: 857 AN: 1984

Alfa AF: 0.454 Hom.: 3496

Bravo AF: 0.390

Asia WGS AF: 0.330 AC: 1137 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	10
DANN	Benign	0.86
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs2176588; hg19: chr2-181261617;