2-187598966-G-A

Variant names:

• chr2-187598966-G-A
• rs4666734

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 0.138 in 151,698 control chromosomes in the GnomAD database, including 1,669 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 0.14 (1669 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.434
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.299 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: 0.138 AC: 20977 AN: 151582 Hom.: 1668 Cov.: 29

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.138 AC: 20985 AN: 151698 Hom.: 1669 Cov.: 29 AF XY: 0.143 AC XY: 10635 AN XY: 74124

African (AFR) AF: 0.138 AC: 5702 AN: 41364

American (AMR) AF: 0.205 AC: 3123 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 526 AN: 3462

East Asian (EAS) AF: 0.312 AC: 1602 AN: 5136

South Asian (SAS) AF: 0.246 AC: 1181 AN: 4808

European-Finnish (FIN) AF: 0.103 AC: 1078 AN: 10500

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7282 AN: 67914

Other (OTH) AF: 0.139 AC: 294 AN: 2110

Alfa AF: 0.0453 Hom.: 42

Bravo AF: 0.143

Asia WGS AF: 0.269 AC: 936 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.7
DANN	Benign	0.86
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs4666734; hg19: chr2-188463693;