ENST00000607039.1:n.1189T>A

Variant names:

• chr1-112463186-T-A
• rs2488787
• ENST00000607039.1:n.1189T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770
• Publications: 4 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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
CTTNBP2NL	ENST00000607039.1	n.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

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

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.800 AC: 16 AN: 20

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.485 AC: 73772 AN: 152070 Hom.: 21604 Cov.: 32 AF XY: 0.486 AC XY: 36098 AN XY: 74342

African (AFR) AF: 0.143 AC: 5940 AN: 41490

American (AMR) AF: 0.549 AC: 8388 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.626 AC: 2171 AN: 3466

East Asian (EAS) AF: 0.442 AC: 2288 AN: 5180

South Asian (SAS) AF: 0.704 AC: 3390 AN: 4816

European-Finnish (FIN) AF: 0.571 AC: 6038 AN: 10566

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.642 AC: 43641 AN: 67960

Other (OTH) AF: 0.551 AC: 1162 AN: 2110

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
PhyloP100		0.077

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2488787; hg19: chr1-113005808;