chr2-601905-T-G

Variant names:

• chr2-601905-T-G
• rs2867105

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 0.841 in 152,250 control chromosomes in the GnomAD database, including 54,047 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 0.84 (54047 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.635
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.898 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: 0.841 AC: 127971 AN: 152132 Hom.: 54011 Cov.: 33

Gnomad AFR AF: 0.876

Gnomad AMI AF: 0.836

Gnomad AMR AF: 0.866

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.919

Gnomad SAS AF: 0.746

Gnomad FIN AF: 0.846

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.821

Gnomad OTH AF: 0.833

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

GnomAD4 genome AF: 0.841 AC: 128062 AN: 152250 Hom.: 54047 Cov.: 33 AF XY: 0.843 AC XY: 62724 AN XY: 74420

African (AFR) AF: 0.876 AC: 36380 AN: 41548

American (AMR) AF: 0.866 AC: 13251 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.724 AC: 2514 AN: 3470

East Asian (EAS) AF: 0.919 AC: 4739 AN: 5154

South Asian (SAS) AF: 0.744 AC: 3591 AN: 4826

European-Finnish (FIN) AF: 0.846 AC: 8979 AN: 10612

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.821 AC: 55839 AN: 68024

Other (OTH) AF: 0.834 AC: 1763 AN: 2114

Alfa AF: 0.824 Hom.: 147219

Bravo AF: 0.846

Asia WGS AF: 0.861 AC: 2994 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.4
DANN	Benign	0.44
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs2867105; hg19: chr2-601905;