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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112268416	XR_002959388.2	n.229-12741C>T		intron_variant	Intron 2 of 3

Ensembl

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

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 v4.3

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;