chr1-116524285-A-G

Position:

• chr1-116524285-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001779.3(CD58):​c.629-2302T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 152,038 control chromosomes in the GnomAD database, including 4,361 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 0.21 (4361 hom., cov: 32)
• Consequence: CD58 NM_001779.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.881

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]

ACMG classification

Verdict is Benign. Variant got -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 = 0.555 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD58	NM_001779.3	c.629-2302T>C		intron_variant		ENST00000369489.10
CD58	NM_001144822.2	c.629-2302T>C		intron_variant
CD58	NR_026665.2	n.683-2302T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD58	ENST00000369489.10	c.629-2302T>C		intron_variant		1	NM_001779.3	A2

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31265 AN: 151920 Hom.: 4346 Cov.: 32

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.0793

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.206 AC: 31313 AN: 152038 Hom.: 4361 Cov.: 32 AF XY: 0.216 AC XY: 16054 AN XY: 74308

Gnomad4 AFR AF: 0.311

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.0793

Gnomad4 EAS AF: 0.572

Gnomad4 SAS AF: 0.372

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.187

Alfa AF: 0.130 Hom.: 2922

Bravo AF: 0.216

Asia WGS AF: 0.448 AC: 1554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.6
DANN	Benign	0.84

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

Other links and lift over

dbSNP: rs1414275; hg19: chr1-117066907;