chr2-129409778-T-C

Variant names:

• chr2-129409778-T-C
• rs985162

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 0.456 in 151,792 control chromosomes in the GnomAD database, including 17,676 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 0.46 (17676 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0780
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.676 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: 0.456 AC: 69126 AN: 151676 Hom.: 17644 Cov.: 32

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.668

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.456 AC: 69212 AN: 151792 Hom.: 17676 Cov.: 32 AF XY: 0.456 AC XY: 33830 AN XY: 74210

African (AFR) AF: 0.682 AC: 28275 AN: 41438

American (AMR) AF: 0.471 AC: 7181 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.377 AC: 1306 AN: 3464

East Asian (EAS) AF: 0.669 AC: 3452 AN: 5158

South Asian (SAS) AF: 0.373 AC: 1794 AN: 4810

European-Finnish (FIN) AF: 0.364 AC: 3828 AN: 10522

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 21996 AN: 67854

Other (OTH) AF: 0.458 AC: 960 AN: 2096

Alfa AF: 0.378 Hom.: 31835

Bravo AF: 0.475

Asia WGS AF: 0.555 AC: 1916 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.4
DANN	Benign	0.63
PhyloP100		-0.078

Splicing

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

Other links and lift over

dbSNP: rs985162; hg19: chr2-130167351;