Genetic Variant NM_012072.4:c.*1660T>C (chr20-23082290-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_012072.4(CD93):c.*1660T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.836 in 152,168 control chromosomes in the GnomAD database, including 53,369 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 0.84 ( 53355 hom., cov: 32)

Exomes 𝑓: 0.91 ( 14 hom. )

Consequence

CD93
NM_012072.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.77

Publications

13 publications found

Variant links:

Genes affected

CD93 (HGNC:15855): (CD93 molecule) The protein encoded by this gene is a cell-surface glycoprotein and type I membrane protein that was originally identified as a myeloid cell-specific marker. The encoded protein was once thought to be a receptor for C1q, but now is thought to instead be involved in intercellular adhesion and in the clearance of apoptotic cells. The intracellular cytoplasmic tail of this protein has been found to interact with moesin, a protein known to play a role in linking transmembrane proteins to the cytoskeleton and in the remodelling of the cytoskeleton. [provided by RefSeq, Jul 2008]

CD93 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=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.932 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD93	NM_012072.4 link	c.*1660T>C		3_prime_UTR_variant	Exon 2 of 2	ENST00000246006.5	NP_036204.2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
CD93	ENST00000246006.5 link	c.*1660T>C	3_prime_UTR_variant	Exon 2 of 2	1	NM_012072.4	ENSP00000246006.4
CD93	ENST00000850633.1 link	n.*368+1292T>C	intron_variant	Intron 2 of 4			ENSP00000520912.1
CD93	ENST00000850634.1 link	n.*122+1538T>C	intron_variant	Intron 2 of 2			ENSP00000520913.1
CD93	ENST00000850635.1 link	n.*122+1538T>C	intron_variant	Intron 2 of 3			ENSP00000520914.1

Frequencies

GnomAD3 genomes

AF:

0.836

AC:

127108

AN:

152018

Hom.:

53323

Cov.:

show subpopulations

Gnomad AFR

AF:

0.808

Gnomad AMI

AF:

0.887

Gnomad AMR

AF:

0.880

Gnomad ASJ

AF:

0.897

Gnomad EAS

AF:

0.954

Gnomad SAS

AF:

0.882

Gnomad FIN

AF:

0.759

Gnomad MID

AF:

0.880

Gnomad NFE

AF:

0.838

Gnomad OTH

AF:

0.868

GnomAD4 exome

AF:

0.912

AC:

AN:

Hom.:

Cov.:

AF XY:

1.00

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.917

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

Variant carriers

<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:

0.836

AC:

127195

AN:

152134

Hom.:

53355

Cov.:

AF XY:

0.834

AC XY:

61978

AN XY:

74358

show subpopulations

African (AFR)

AF:

0.808

AC:

33505

AN:

41470

American (AMR)

AF:

0.880

AC:

13463

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.897

AC:

3113

AN:

3472

East Asian (EAS)

AF:

0.954

AC:

4941

AN:

5178

South Asian (SAS)

AF:

0.883

AC:

4259

AN:

4822

European-Finnish (FIN)

AF:

0.759

AC:

8021

AN:

10564

Middle Eastern (MID)

AF:

0.878

AC:

258

AN:

294

European-Non Finnish (NFE)

AF:

0.838

AC:

56992

AN:

68012

Other (OTH)

AF:

0.868

AC:

1834

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1077

2154

3231

4308

5385

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

888

1776

2664

3552

4440

<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:

0.840

Hom.:

46550

Bravo

AF:

0.846

Asia WGS

AF:

0.913

AC:

3175

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.21

(source)

DANN

Benign

0.43

PhyloP100

-1.8

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

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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