rs2278664

Variant summary

Our verdict is Benign. Variant got -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

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.214
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons MANE UniProt
CABYRNM_153769.3 linkuse as main transcriptc.-25+245C>T intron_variant ENST00000399496.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CABYRENST00000399496.8 linkuse as main transcriptc.-25+245C>T intron_variant 1 NM_153769.3 P1O75952-3

Frequencies

GnomAD3 genomes
AF:
0.472
AC:
71690
AN:
151834
Hom.:
20397
Cov.:
31
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:
66
AN:
102
Hom.:
24
AF XY:
0.654
AC XY:
51
AN XY:
78
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
1.00
Gnomad4 EAS exome
AF:
0.250
Gnomad4 FIN exome
AF:
0.400
Gnomad4 NFE exome
AF:
0.711
Gnomad4 OTH exome
AF:
0.625
GnomAD4 genome
AF:
0.472
AC:
71693
AN:
151954
Hom.:
20397
Cov.:
31
AF XY:
0.470
AC XY:
34858
AN XY:
74220
show subpopulations
Gnomad4 AFR
AF:
0.146
Gnomad4 AMR
AF:
0.511
Gnomad4 ASJ
AF:
0.610
Gnomad4 EAS
AF:
0.396
Gnomad4 SAS
AF:
0.454
Gnomad4 FIN
AF:
0.580
Gnomad4 NFE
AF:
0.643
Gnomad4 OTH
AF:
0.523
Alfa
AF:
0.610
Hom.:
38255
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
DANN
Benign
0.78

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

LitVar

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

Other links and lift over

dbSNP: rs2278664; hg19: chr18-21719327; API