2-55865477-C-T

Variant names:

• chr2-55865477-C-T
• rs1346787
• XR_002959388.2:n.229-8406C>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.229-8406C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.658 in 151,910 control chromosomes in the GnomAD database, including 34,628 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 0.66 (34628 hom., cov: 30)
• Consequence: LOC112268416 XR_002959388.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.876 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: 0.657 AC: 99791 AN: 151792 Hom.: 34587 Cov.: 30

Gnomad AFR AF: 0.860

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.737

Gnomad EAS AF: 0.897

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.658 AC: 99890 AN: 151910 Hom.: 34628 Cov.: 30 AF XY: 0.654 AC XY: 48558 AN XY: 74224

African (AFR) AF: 0.860 AC: 35659 AN: 41456

American (AMR) AF: 0.538 AC: 8201 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.737 AC: 2557 AN: 3468

East Asian (EAS) AF: 0.897 AC: 4640 AN: 5172

South Asian (SAS) AF: 0.678 AC: 3259 AN: 4810

European-Finnish (FIN) AF: 0.440 AC: 4622 AN: 10514

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.569 AC: 38662 AN: 67922

Other (OTH) AF: 0.673 AC: 1418 AN: 2106

Alfa AF: 0.587 Hom.: 42354

Bravo AF: 0.671

Asia WGS AF: 0.784 AC: 2728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.1
DANN	Benign	0.56
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs1346787; hg19: chr2-56092612;