2-67412637-G-T

Variant names:

• chr2-67412637-G-T
• rs1486134

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 0.737 in 151,958 control chromosomes in the GnomAD database, including 41,686 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 0.74 (41686 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.918
• Publications: 26 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.823 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: 0.737 AC: 111927 AN: 151840 Hom.: 41662 Cov.: 31

Gnomad AFR AF: 0.831

Gnomad AMI AF: 0.751

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.711

Gnomad OTH AF: 0.769

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

GnomAD4 genome AF: 0.737 AC: 112008 AN: 151958 Hom.: 41686 Cov.: 31 AF XY: 0.732 AC XY: 54367 AN XY: 74268

African (AFR) AF: 0.831 AC: 34475 AN: 41494

American (AMR) AF: 0.713 AC: 10855 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.776 AC: 2692 AN: 3468

East Asian (EAS) AF: 0.585 AC: 3012 AN: 5150

South Asian (SAS) AF: 0.710 AC: 3417 AN: 4816

European-Finnish (FIN) AF: 0.637 AC: 6719 AN: 10556

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.711 AC: 48306 AN: 67932

Other (OTH) AF: 0.767 AC: 1614 AN: 2104

Alfa AF: 0.721 Hom.: 114741

Bravo AF: 0.745

Asia WGS AF: 0.698 AC: 2428 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	9.0
DANN	Benign	0.54
PhyloP100		0.92

Splicing

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

Other links and lift over

dbSNP: rs1486134; hg19: chr2-67639769;