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GeneBe

1-116768672-G-A

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_001767.5(CD2):c.945G>A(p.Pro315=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00142 in 1,614,050 control chromosomes in the GnomAD database, including 27 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0070 ( 15 hom., cov: 31)
Exomes 𝑓: 0.00083 ( 12 hom. )

Consequence

CD2
NM_001767.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -3.37
Variant links:
Genes affected
CD2 (HGNC:1639): (CD2 molecule) The protein encoded by this gene is a surface antigen found on all peripheral blood T-cells. The encoded protein interacts with LFA3 (CD58) on antigen presenting cells to optimize immune recognition. A locus control region (LCR) has been found in the 3' flanking sequence of this gene. [provided by RefSeq, Jun 2016]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 1-116768672-G-A is Benign according to our data. Variant chr1-116768672-G-A is described in ClinVar as [Benign]. Clinvar id is 791111.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-3.37 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00705 (1072/152160) while in subpopulation AFR AF= 0.024 (995/41498). AF 95% confidence interval is 0.0227. There are 15 homozygotes in gnomad4. There are 504 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 15 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CD2NM_001767.5 linkuse as main transcriptc.945G>A p.Pro315= synonymous_variant 5/5 ENST00000369478.4
CD2NM_001328609.2 linkuse as main transcriptc.1023G>A p.Pro341= synonymous_variant 5/5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CD2ENST00000369478.4 linkuse as main transcriptc.945G>A p.Pro315= synonymous_variant 5/51 NM_001767.5 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00699
AC:
1063
AN:
152042
Hom.:
15
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0239
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00255
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.000208
Gnomad FIN
AF:
0.0000943
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000279
Gnomad OTH
AF:
0.00717
GnomAD3 exomes
AF:
0.00188
AC:
473
AN:
251264
Hom.:
9
AF XY:
0.00127
AC XY:
173
AN XY:
135838
show subpopulations
Gnomad AFR exome
AF:
0.0242
Gnomad AMR exome
AF:
0.00136
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000653
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000203
Gnomad OTH exome
AF:
0.00114
GnomAD4 exome
AF:
0.000835
AC:
1220
AN:
1461890
Hom.:
12
Cov.:
31
AF XY:
0.000733
AC XY:
533
AN XY:
727248
show subpopulations
Gnomad4 AFR exome
AF:
0.0237
Gnomad4 AMR exome
AF:
0.00161
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000504
Gnomad4 SAS exome
AF:
0.0000696
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000221
Gnomad4 OTH exome
AF:
0.00146
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00705
AC:
1072
AN:
152160
Hom.:
15
Cov.:
31
AF XY:
0.00678
AC XY:
504
AN XY:
74380
show subpopulations
Gnomad4 AFR
AF:
0.0240
Gnomad4 AMR
AF:
0.00255
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.000208
Gnomad4 FIN
AF:
0.0000943
Gnomad4 NFE
AF:
0.000279
Gnomad4 OTH
AF:
0.00710
Alfa
AF:
0.00290
Hom.:
5
Bravo
AF:
0.00794
Asia WGS
AF:
0.00173
AC:
6
AN:
3478
EpiCase
AF:
0.0000545
EpiControl
AF:
0.000119

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeApr 23, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.76
Cadd
Benign
1.6
Dann
Benign
0.59

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs35591188; hg19: chr1-117311294; COSMIC: COSV65644854; API