dbSNP rs1016140: CD58:c.628+2040C>A (chr1-116533925-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001779.3(CD58):c.628+2040C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 1,395,176 control chromosomes in the GnomAD database, including 20,905 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 0.16 ( 2632 hom., cov: 32)

Exomes 𝑓: 0.13 ( 18273 hom. )

Consequence

CD58
NM_001779.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0110

Publications

19 publications found

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]

CD58 links:

NAP1L4P1 (HGNC:39740): (nucleosome assembly protein 1 like 4 pseudogene 1)

NAP1L4P1 links:

ENSG00000298543 (HGNC:):

ENSG00000298543 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
CD58	NM_001779.3 link	c.628+2040C>A	intron_variant	Intron 3 of 5	ENST00000369489.10	NP_001770.1	P19256-1
NAP1L4P1		n.116533925G>T	intragenic_variant
CD58	NM_001144822.2 link	c.628+2040C>A	intron_variant	Intron 3 of 4		NP_001138294.1	P19256-3
CD58	NR_026665.2 link	n.682+2040C>A	intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD58	ENST00000369489.10 link	c.628+2040C>A		intron_variant	Intron 3 of 5	1	NM_001779.3	ENSP00000358501.5		P19256-1

Frequencies

GnomAD3 genomes

AF:

0.157

AC:

23813

AN:

151992

Hom.:

2629

Cov.:

show subpopulations

Gnomad AFR

AF:

0.144

Gnomad AMI

AF:

0.157

Gnomad AMR

AF:

0.238

Gnomad ASJ

AF:

0.0766

Gnomad EAS

AF:

0.572

Gnomad SAS

AF:

0.335

Gnomad FIN

AF:

0.173

Gnomad MID

AF:

0.114

Gnomad NFE

AF:

0.104

Gnomad OTH

AF:

0.155

GnomAD4 exome

AF:

0.131

AC:

162870

AN:

1243066

Hom.:

18273

Cov.:

AF XY:

0.136

AC XY:

85390

AN XY:

628140

show subpopulations

African (AFR)

AF:

0.132

AC:

3770

AN:

28586

American (AMR)

AF:

0.323

AC:

14177

AN:

43886

Ashkenazi Jewish (ASJ)

AF:

0.0714

AC:

1761

AN:

24648

East Asian (EAS)

AF:

0.576

AC:

21583

AN:

37462

South Asian (SAS)

AF:

0.307

AC:

24710

AN:

80456

European-Finnish (FIN)

AF:

0.156

AC:

8005

AN:

51380

Middle Eastern (MID)

AF:

0.123

AC:

641

AN:

5204

European-Non Finnish (NFE)

AF:

0.0879

AC:

80841

AN:

919240

Other (OTH)

AF:

0.141

AC:

7382

AN:

52204

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.434

Heterozygous variant carriers

4868

9737

14605

19474

24342

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2948

5896

8844

11792

14740

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.157

AC:

23829

AN:

152110

Hom.:

2632

Cov.:

AF XY:

0.168

AC XY:

12477

AN XY:

74350

show subpopulations

African (AFR)

AF:

0.144

AC:

5957

AN:

41490

American (AMR)

AF:

0.238

AC:

3639

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.0766

AC:

266

AN:

3472

East Asian (EAS)

AF:

0.572

AC:

2960

AN:

5176

South Asian (SAS)

AF:

0.336

AC:

1618

AN:

4818

European-Finnish (FIN)

AF:

0.173

AC:

1828

AN:

10558

Middle Eastern (MID)

AF:

0.112

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.104

AC:

7055

AN:

68008

Other (OTH)

AF:

0.157

AC:

331

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

936

1873

2809

3746

4682

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

270

540

810

1080

1350

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.127

Hom.:

388

Bravo

AF:

0.161

Asia WGS

AF:

0.404

AC:

1402

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.29

(source)

DANN

Benign

0.65

PhyloP100

-0.011

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over