rs4129068

chr2-226429766-C-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 0.13 in 152,254 control chromosomes in the GnomAD database, including 1,591 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 0.13 (1591 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19762 AN: 152136 Hom.: 1587 Cov.: 32

Gnomad AFR AF: 0.0412

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.0947

Gnomad SAS AF: 0.0695

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.220

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.130 AC: 19774 AN: 152254 Hom.: 1591 Cov.: 32 AF XY: 0.129 AC XY: 9600 AN XY: 74434

Gnomad4 AFR AF: 0.0411

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.0947

Gnomad4 SAS AF: 0.0685

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.170

Alfa AF: 0.167 Hom.: 3002

Bravo AF: 0.125

Asia WGS AF: 0.131 AC: 455 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.089
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4129068; hg19: chr2-227294482;