4-126287562-A-G

Variant names:

• chr4-126287562-A-G
• rs2128782

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 0.723 in 151,184 control chromosomes in the GnomAD database, including 39,715 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 0.72 (39715 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.785 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: 0.723 AC: 109292 AN: 151066 Hom.: 39695 Cov.: 31

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.736

Gnomad ASJ AF: 0.676

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.807

Gnomad FIN AF: 0.654

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.717

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.723 AC: 109364 AN: 151184 Hom.: 39715 Cov.: 31 AF XY: 0.723 AC XY: 53422 AN XY: 73862

African (AFR) AF: 0.750 AC: 31042 AN: 41386

American (AMR) AF: 0.737 AC: 11141 AN: 15126

Ashkenazi Jewish (ASJ) AF: 0.676 AC: 2333 AN: 3452

East Asian (EAS) AF: 0.691 AC: 3539 AN: 5120

South Asian (SAS) AF: 0.806 AC: 3878 AN: 4810

European-Finnish (FIN) AF: 0.654 AC: 6900 AN: 10556

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.717 AC: 48350 AN: 67432

Other (OTH) AF: 0.689 AC: 1446 AN: 2100

Alfa AF: 0.718 Hom.: 61694

Bravo AF: 0.728

Asia WGS AF: 0.771 AC: 2678 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.6
DANN	Benign	0.68
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs2128782; hg19: chr4-127208717;