rs2488787

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000607039.1(CTTNBP2NL):​n.1189T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 152,094 control chromosomes in the GnomAD database, including 21,611 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 0.49 ( 21604 hom., cov: 32)
Exomes 𝑓: 0.67 ( 7 hom. )

Consequence

CTTNBP2NL
ENST00000607039.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0770
Variant links:
Genes affected
CTTNBP2NL (HGNC:25330): (CTTNBP2 N-terminal like) Enables protein phosphatase 2A binding activity. Acts upstream of or within negative regulation of transmembrane transport; negative regulation of transporter activity; and protein dephosphorylation. Located in actin cytoskeleton. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.83).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CTTNBP2NLENST00000607039.1 linkn.1189T>A non_coding_transcript_exon_variant Exon 2 of 2 1

Frequencies

GnomAD3 genomes
AF:
0.485
AC:
73764
AN:
151952
Hom.:
21599
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.144
Gnomad AMI
AF:
0.640
Gnomad AMR
AF:
0.549
Gnomad ASJ
AF:
0.626
Gnomad EAS
AF:
0.441
Gnomad SAS
AF:
0.703
Gnomad FIN
AF:
0.571
Gnomad MID
AF:
0.589
Gnomad NFE
AF:
0.642
Gnomad OTH
AF:
0.547
GnomAD4 exome
AF:
0.667
AC:
16
AN:
24
Hom.:
7
Cov.:
0
AF XY:
0.750
AC XY:
9
AN XY:
12
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.800
GnomAD4 genome
AF:
0.485
AC:
73772
AN:
152070
Hom.:
21604
Cov.:
32
AF XY:
0.486
AC XY:
36098
AN XY:
74342
show subpopulations
Gnomad4 AFR
AF:
0.143
Gnomad4 AMR
AF:
0.549
Gnomad4 ASJ
AF:
0.626
Gnomad4 EAS
AF:
0.442
Gnomad4 SAS
AF:
0.704
Gnomad4 FIN
AF:
0.571
Gnomad4 NFE
AF:
0.642
Gnomad4 OTH
AF:
0.551
Alfa
AF:
0.540
Hom.:
2983
Bravo
AF:
0.465
Asia WGS
AF:
0.523
AC:
1821
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
3.5
DANN
Benign
0.84

Splicing

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: rs2488787; hg19: chr1-113005808; API