2-614210-A-G

Variant names:

• chr2-614210-A-G
• rs2860323

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 0.856 in 152,128 control chromosomes in the GnomAD database, including 55,905 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 0.86 (55905 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.902 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: 0.856 AC: 130132 AN: 152010 Hom.: 55864 Cov.: 31

Gnomad AFR AF: 0.910

Gnomad AMI AF: 0.822

Gnomad AMR AF: 0.872

Gnomad ASJ AF: 0.744

Gnomad EAS AF: 0.920

Gnomad SAS AF: 0.801

Gnomad FIN AF: 0.847

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.827

Gnomad OTH AF: 0.853

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

GnomAD4 genome AF: 0.856 AC: 130230 AN: 152128 Hom.: 55905 Cov.: 31 AF XY: 0.858 AC XY: 63776 AN XY: 74350

African (AFR) AF: 0.910 AC: 37767 AN: 41514

American (AMR) AF: 0.872 AC: 13338 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.744 AC: 2583 AN: 3470

East Asian (EAS) AF: 0.920 AC: 4755 AN: 5166

South Asian (SAS) AF: 0.799 AC: 3853 AN: 4824

European-Finnish (FIN) AF: 0.847 AC: 8953 AN: 10566

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.827 AC: 56186 AN: 67980

Other (OTH) AF: 0.854 AC: 1803 AN: 2112

Alfa AF: 0.843 Hom.: 21045

Bravo AF: 0.861

Asia WGS AF: 0.871 AC: 3032 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.77
DANN	Benign	0.13
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2860323; hg19: chr2-614210;