rs2128782

Variant names:

• chr4-126287562-A-G
• rs2128782

Your query was ambiguous. Multiple possible variants found:

• chr4-126287562-A-G
• chr4-126287562-A-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.750

Gnomad4 AMR AF: 0.737

Gnomad4 ASJ AF: 0.676

Gnomad4 EAS AF: 0.691

Gnomad4 SAS AF: 0.806

Gnomad4 FIN AF: 0.654

Gnomad4 NFE AF: 0.717

Gnomad4 OTH AF: 0.689

Alfa AF: 0.717 Hom.: 49305

Bravo AF: 0.728

Asia WGS AF: 0.771 AC: 2678 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2128782; hg19: chr4-127208717;