2-55861142-C-T

Variant names:

• chr2-55861142-C-T
• rs4352264
• XR_002959388.2:n.229-12741C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_002959388.2(LOC112268416):​n.229-12741C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.533 in 151,970 control chromosomes in the GnomAD database, including 22,995 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 0.53 (22995 hom., cov: 32)
• Consequence: LOC112268416 XR_002959388.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.52
• Publications: 9 publications found

Genes affected

LOC112268416 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.873 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: 0.533 AC: 80945 AN: 151850 Hom.: 22967 Cov.: 32

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.541

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.895

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.638

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.533 AC: 81029 AN: 151970 Hom.: 22995 Cov.: 32 AF XY: 0.536 AC XY: 39791 AN XY: 74304

African (AFR) AF: 0.693 AC: 28714 AN: 41424

American (AMR) AF: 0.443 AC: 6766 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.540 AC: 1874 AN: 3472

East Asian (EAS) AF: 0.895 AC: 4621 AN: 5164

South Asian (SAS) AF: 0.630 AC: 3032 AN: 4814

European-Finnish (FIN) AF: 0.365 AC: 3856 AN: 10574

Middle Eastern (MID) AF: 0.617 AC: 179 AN: 290

European-Non Finnish (NFE) AF: 0.446 AC: 30326 AN: 67958

Other (OTH) AF: 0.556 AC: 1171 AN: 2108

Alfa AF: 0.486 Hom.: 3837

Bravo AF: 0.543

Asia WGS AF: 0.752 AC: 2615 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	13
DANN	Benign	0.86
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs4352264; hg19: chr2-56088277;