chr2-137962853-C-T

Variant names:

• chr2-137962853-C-T
• rs6430764

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 0.534 in 152,058 control chromosomes in the GnomAD database, including 22,342 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 0.53 (22342 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.613 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: 0.534 AC: 81150 AN: 151938 Hom.: 22335 Cov.: 34

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.460

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.534 AC: 81190 AN: 152058 Hom.: 22342 Cov.: 34 AF XY: 0.533 AC XY: 39637 AN XY: 74332

African (AFR) AF: 0.399 AC: 16554 AN: 41448

American (AMR) AF: 0.623 AC: 9521 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1632 AN: 3466

East Asian (EAS) AF: 0.621 AC: 3214 AN: 5172

South Asian (SAS) AF: 0.577 AC: 2779 AN: 4816

European-Finnish (FIN) AF: 0.512 AC: 5412 AN: 10568

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.594 AC: 40415 AN: 68000

Other (OTH) AF: 0.523 AC: 1104 AN: 2110

Alfa AF: 0.567 Hom.: 28900

Bravo AF: 0.538

Asia WGS AF: 0.568 AC: 1975 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-1.8

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6430764; hg19: chr2-138720423;