rs2488787

Positions:

• chr1-112463186-T-A
• chr1-112463186-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CTTNBP2NL	ENST00000607039.1	n.1189T>A		non_coding_transcript_exon_variant	2/2	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

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

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

Other links and lift over

dbSNP: rs2488787; hg19: chr1-113005808;