chr1-116558335-A-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001779.3(CD58):​c.70+12568T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)

Consequence

CD58
NM_001779.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.140
Variant links:
Genes affected
CD58 (HGNC:1688): (CD58 molecule) This gene encodes a member of the immunoglobulin superfamily. The encoded protein is a ligand of the T lymphocyte CD2 protein, and functions in adhesion and activation of T lymphocytes. The protein is localized to the plasma membrane. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jan 2009]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.78).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CD58NM_001779.3 linkuse as main transcriptc.70+12568T>A intron_variant ENST00000369489.10
LOC105378925XR_947739.2 linkuse as main transcriptn.8158A>T non_coding_transcript_exon_variant 3/3
CD58NM_001144822.2 linkuse as main transcriptc.70+12568T>A intron_variant
CD58NR_026665.2 linkuse as main transcriptn.124+12568T>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CD58ENST00000369489.10 linkuse as main transcriptc.70+12568T>A intron_variant 1 NM_001779.3 A2P19256-1
CD58ENST00000369487.3 linkuse as main transcriptc.70+12568T>A intron_variant 1 P4
CD58ENST00000457047.6 linkuse as main transcriptc.70+12568T>A intron_variant 1 A2P19256-3
CD58ENST00000464088.5 linkuse as main transcriptc.70+12568T>A intron_variant, NMD_transcript_variant 1 P19256-2

Frequencies

GnomAD3 genomes
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.78
CADD
Benign
6.9
DANN
Benign
0.88

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1335532; hg19: chr1-117100957; API