NM_001779.3:c.71-553G>T

Variant names:

• chr1-116545157-C-A
• rs12044852
• NM_001779.3:c.71-553G>T

Variant summary

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

The NM_001779.3(CD58):​c.71-553G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,026 control chromosomes in the GnomAD database, including 2,183 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 0.13 (2183 hom., cov: 32)
• Consequence: CD58 NM_001779.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.405
• Publications: 35 publications found

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]

ENSG00000298543 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD58	NM_001779.3	c.71-553G>T		intron_variant	Intron 1 of 5	ENST00000369489.10	NP_001770.1
CD58	NM_001144822.2	c.71-553G>T		intron_variant	Intron 1 of 4		NP_001138294.1
CD58	NR_026665.2	n.125-553G>T		intron_variant	Intron 1 of 5
LOC105378925	XR_947739.2	n.124+333C>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD58	ENST00000369489.10	c.71-553G>T		intron_variant	Intron 1 of 5	1	NM_001779.3	ENSP00000358501.5

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19950 AN: 151908 Hom.: 2183 Cov.: 32

Gnomad AFR AF: 0.0665

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.0741

Gnomad EAS AF: 0.566

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.131 AC: 19956 AN: 152026 Hom.: 2183 Cov.: 32 AF XY: 0.142 AC XY: 10554 AN XY: 74318

African (AFR) AF: 0.0665 AC: 2758 AN: 41470

American (AMR) AF: 0.222 AC: 3395 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0741 AC: 257 AN: 3468

East Asian (EAS) AF: 0.565 AC: 2908 AN: 5144

South Asian (SAS) AF: 0.332 AC: 1598 AN: 4812

European-Finnish (FIN) AF: 0.157 AC: 1662 AN: 10568

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.102 AC: 6929 AN: 67970

Other (OTH) AF: 0.132 AC: 279 AN: 2110

Alfa AF: 0.117 Hom.: 3909

Bravo AF: 0.133

Asia WGS AF: 0.393 AC: 1361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.2
DANN	Benign	0.45
PhyloP100		0.41
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12044852; hg19: chr1-117087779;