Genetic Variant CABYR:c.-25+245C>T (chr18-24139363-C-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_153769.3(CABYR):c.-25+245C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.472 in 152,056 control chromosomes in the GnomAD database, including 20,421 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 0.47 ( 20397 hom., cov: 31)

Exomes 𝑓: 0.65 ( 24 hom. )

Consequence

CABYR
NM_153769.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.214

Publications

13 publications found

Variant links:

Genes affected

CABYR (HGNC:15569): (calcium binding tyrosine phosphorylation regulated) To reach fertilization competence, spermatozoa undergo a series of morphological and molecular maturational processes, termed capacitation, involving protein tyrosine phosphorylation and increased intracellular calcium. The protein encoded by this gene localizes to the principal piece of the sperm flagellum in association with the fibrous sheath and exhibits calcium-binding when phosphorylated during capacitation. A pseudogene on chromosome 3 has been identified for this gene. Alternatively spliced transcript variants encoding distinct protein isoforms have been found for this gene. [provided by RefSeq, Jul 2013]

CABYR links:

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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=-0.75).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CABYR	NM_153769.3 link	c.-25+245C>T		intron_variant	Intron 1 of 5	ENST00000399496.8	NP_722453.1	O75952-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CABYR	ENST00000399496.8 link	c.-25+245C>T		intron_variant	Intron 1 of 5	1	NM_153769.3	ENSP00000382419.3		O75952-3

Frequencies

GnomAD3 genomes

AF:

0.472

AC:

71690

AN:

151834

Hom.:

20397

Cov.:

show subpopulations

Gnomad AFR

AF:

0.146

Gnomad AMI

AF:

0.515

Gnomad AMR

AF:

0.512

Gnomad ASJ

AF:

0.610

Gnomad EAS

AF:

0.397

Gnomad SAS

AF:

0.453

Gnomad FIN

AF:

0.580

Gnomad MID

AF:

0.491

Gnomad NFE

AF:

0.643

Gnomad OTH

AF:

0.521

GnomAD4 exome

AF:

0.647

AC:

AN:

102

Hom.:

AF XY:

0.654

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

1.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.250

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.400

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.711

AC:

AN:

Other (OTH)

AF:

0.625

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.472

AC:

71693

AN:

151954

Hom.:

20397

Cov.:

AF XY:

0.470

AC XY:

34858

AN XY:

74220

show subpopulations

African (AFR)

AF:

0.146

AC:

6063

AN:

41472

American (AMR)

AF:

0.511

AC:

7817

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.610

AC:

2117

AN:

3468

East Asian (EAS)

AF:

0.396

AC:

2028

AN:

5122

South Asian (SAS)

AF:

0.454

AC:

2188

AN:

4816

European-Finnish (FIN)

AF:

0.580

AC:

6108

AN:

10536

Middle Eastern (MID)

AF:

0.473

AC:

139

AN:

294

European-Non Finnish (NFE)

AF:

0.643

AC:

43665

AN:

67950

Other (OTH)

AF:

0.523

AC:

1102

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1596

3191

4787

6382

7978

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

624

1248

1872

2496

3120

<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:

0.594

Hom.:

46520

Bravo

AF:

0.449

Asia WGS

AF:

0.436

AC:

1514

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

7.1

(source)

DANN

Benign

0.78

PhyloP100

0.21

PromoterAI

0.25

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over