2-6114620-A-G

Variant names:

• chr2-6114620-A-G
• rs2693889

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 0.196 in 152,126 control chromosomes in the GnomAD database, including 5,870 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 (5870 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.493 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: 0.195 AC: 29717 AN: 152008 Hom.: 5849 Cov.: 32

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0886

Gnomad ASJ AF: 0.0813

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0524

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0593

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.196 AC: 29776 AN: 152126 Hom.: 5870 Cov.: 32 AF XY: 0.193 AC XY: 14345 AN XY: 74392

African (AFR) AF: 0.498 AC: 20656 AN: 41462

American (AMR) AF: 0.0884 AC: 1351 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0813 AC: 282 AN: 3470

East Asian (EAS) AF: 0.382 AC: 1970 AN: 5154

South Asian (SAS) AF: 0.101 AC: 486 AN: 4828

European-Finnish (FIN) AF: 0.0524 AC: 556 AN: 10620

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.0593 AC: 4033 AN: 67988

Other (OTH) AF: 0.164 AC: 347 AN: 2110

Alfa AF: 0.0970 Hom.: 7631

Bravo AF: 0.214

Asia WGS AF: 0.233 AC: 811 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.43
DANN	Benign	0.63
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2693889; hg19: chr2-6254752;