rs4129068

Variant names:

• chr2-226429766-C-T
• rs4129068

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 0.13 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
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0411 AC: 1707 AN: 41564

American (AMR) AF: 0.162 AC: 2482 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 811 AN: 3470

East Asian (EAS) AF: 0.0947 AC: 491 AN: 5184

South Asian (SAS) AF: 0.0685 AC: 331 AN: 4830

European-Finnish (FIN) AF: 0.193 AC: 2046 AN: 10592

Middle Eastern (MID) AF: 0.219 AC: 64 AN: 292

European-Non Finnish (NFE) AF: 0.167 AC: 11387 AN: 68014

Other (OTH) AF: 0.170 AC: 358 AN: 2112

Alfa AF: 0.163 Hom.: 3627

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
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs4129068; hg19: chr2-227294482;