1-116561593-A-G

Variant names:

• chr1-116561593-A-G
• rs2300747
• NM_001779.3:c.70+9310T>C

Variant summary

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

The NM_001779.3(CD58):​c.70+9310T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 152,162 control chromosomes in the GnomAD database, including 3,916 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 0.20 (3916 hom., cov: 32)
• Consequence: CD58 NM_001779.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.229
• Publications: 83 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.588 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001779.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD58	NM_001779.3	MANE Select	c.70+9310T>C		intron	N/A	NP_001770.1
	CD58	NM_001144822.2		c.70+9310T>C		intron	N/A	NP_001138294.1
	CD58	NR_026665.2		n.124+9310T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD58	ENST00000369489.10	TSL:1 MANE Select	c.70+9310T>C		intron	N/A	ENSP00000358501.5
	CD58	ENST00000457047.6	TSL:1	c.70+9310T>C		intron	N/A	ENSP00000409080.2
	CD58	ENST00000369487.3	TSL:1	c.70+9310T>C		intron	N/A	ENSP00000358499.3

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30665 AN: 152044 Hom.: 3905 Cov.: 32

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.0833

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.202 AC: 30717 AN: 152162 Hom.: 3916 Cov.: 32 AF XY: 0.213 AC XY: 15851 AN XY: 74394

African (AFR) AF: 0.240 AC: 9977 AN: 41504

American (AMR) AF: 0.275 AC: 4197 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0833 AC: 289 AN: 3470

East Asian (EAS) AF: 0.605 AC: 3135 AN: 5178

South Asian (SAS) AF: 0.361 AC: 1739 AN: 4822

European-Finnish (FIN) AF: 0.200 AC: 2124 AN: 10594

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8654 AN: 68002

Other (OTH) AF: 0.198 AC: 420 AN: 2116

Alfa AF: 0.160 Hom.: 9881

Bravo AF: 0.207

Asia WGS AF: 0.441 AC: 1529 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.95
DANN	Benign	0.73
PhyloP100		-0.23
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2300747; hg19: chr1-117104215;