rs4668059

Variant names:

• chr2-168309772-T-C
• rs4668059

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 0.109 in 152,194 control chromosomes in the GnomAD database, including 1,135 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 0.11 (1135 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.203 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: 0.109 AC: 16516 AN: 152076 Hom.: 1138 Cov.: 32

Gnomad AFR AF: 0.0348

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.0823

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.109 AC: 16514 AN: 152194 Hom.: 1135 Cov.: 32 AF XY: 0.109 AC XY: 8081 AN XY: 74390

African (AFR) AF: 0.0347 AC: 1442 AN: 41540

American (AMR) AF: 0.190 AC: 2900 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 365 AN: 3472

East Asian (EAS) AF: 0.214 AC: 1102 AN: 5152

South Asian (SAS) AF: 0.201 AC: 970 AN: 4814

European-Finnish (FIN) AF: 0.0823 AC: 872 AN: 10598

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8438 AN: 68022

Other (OTH) AF: 0.130 AC: 275 AN: 2114

Alfa AF: 0.125 Hom.: 2440

Bravo AF: 0.113

Asia WGS AF: 0.190 AC: 659 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	11
DANN	Benign	0.89
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs4668059; hg19: chr2-169166282;