2-126902405-T-C

Variant names:

• chr2-126902405-T-C
• rs6733840

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 0.253 in 152,152 control chromosomes in the GnomAD database, including 7,615 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 0.25 (7615 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.492
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.546 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: 0.252 AC: 38364 AN: 152032 Hom.: 7589 Cov.: 32

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.0742

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.253 AC: 38442 AN: 152152 Hom.: 7615 Cov.: 32 AF XY: 0.248 AC XY: 18449 AN XY: 74392

African (AFR) AF: 0.552 AC: 22886 AN: 41476

American (AMR) AF: 0.176 AC: 2699 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 756 AN: 3472

East Asian (EAS) AF: 0.157 AC: 814 AN: 5174

South Asian (SAS) AF: 0.214 AC: 1033 AN: 4816

European-Finnish (FIN) AF: 0.0742 AC: 786 AN: 10596

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8692 AN: 67998

Other (OTH) AF: 0.250 AC: 529 AN: 2114

Alfa AF: 0.199 Hom.: 780

Bravo AF: 0.275

Asia WGS AF: 0.258 AC: 898 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.87
DANN	Benign	0.40
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs6733840; hg19: chr2-127659981;