rs2077386

Variant names:

• chr2-231931043-G-C
• rs2077386

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 0.201 in 151,944 control chromosomes in the GnomAD database, including 4,171 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 0.20 (4171 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.159
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30481 AN: 151826 Hom.: 4157 Cov.: 31

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.0824

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.0422

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.201 AC: 30540 AN: 151944 Hom.: 4171 Cov.: 31 AF XY: 0.199 AC XY: 14738 AN XY: 74246

African (AFR) AF: 0.382 AC: 15838 AN: 41408

American (AMR) AF: 0.202 AC: 3081 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 538 AN: 3470

East Asian (EAS) AF: 0.0423 AC: 218 AN: 5150

South Asian (SAS) AF: 0.206 AC: 989 AN: 4804

European-Finnish (FIN) AF: 0.118 AC: 1249 AN: 10560

Middle Eastern (MID) AF: 0.127 AC: 37 AN: 292

European-Non Finnish (NFE) AF: 0.119 AC: 8112 AN: 67988

Other (OTH) AF: 0.192 AC: 403 AN: 2104

Alfa AF: 0.171 Hom.: 397

Bravo AF: 0.216

Asia WGS AF: 0.160 AC: 558 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.5
DANN	Benign	0.51
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs2077386; hg19: chr2-232795753;