1-116545157-C-A

Position:

• chr1-116545157-C-A

Variant summary

Our verdict is Benign. Variant got -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

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]

LOC105378925 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
CD58	NM_001779.3	c.71-553G>T		intron_variant		ENST00000369489.10	NP_001770.1
LOC105378925	XR_947739.2	n.124+333C>A		intron_variant, non_coding_transcript_variant
CD58	NM_001144822.2	c.71-553G>T		intron_variant			NP_001138294.1
CD58	NR_026665.2	n.125-553G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD58	ENST00000369489.10	c.71-553G>T		intron_variant		1	NM_001779.3	ENSP00000358501	A2
CD58	ENST00000369487.3	c.71-553G>T		intron_variant		1		ENSP00000358499	P4
CD58	ENST00000457047.6	c.71-553G>T		intron_variant		1		ENSP00000409080	A2
CD58	ENST00000464088.5	c.71-553G>T		intron_variant, NMD_transcript_variant		1		ENSP00000432773

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

Gnomad4 AFR AF: 0.0665

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.0741

Gnomad4 EAS AF: 0.565

Gnomad4 SAS AF: 0.332

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.132

Alfa AF: 0.114 Hom.: 1347

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

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: rs12044852; hg19: chr1-117087779;