chr1-112459858-G-A

Position:

• chr1-112459858-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_018704.3(CTTNBP2NL):​c.*2446G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 152,158 control chromosomes in the GnomAD database, including 4,077 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 0.21 (4077 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: CTTNBP2NL NM_018704.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.44

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]

CTTNBP2NL (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.535 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CTTNBP2NL	NM_018704.3	c.*2446G>A		3_prime_UTR_variant	6/6	ENST00000271277.11	NP_061174.1
CTTNBP2NL	XM_011541781.3	c.*2446G>A		3_prime_UTR_variant	6/6		XP_011540083.1
CTTNBP2NL	XM_017001806.2	c.*2446G>A		3_prime_UTR_variant	6/6		XP_016857295.1
CTTNBP2NL	XM_047425362.1	c.*2446G>A		3_prime_UTR_variant	6/6		XP_047281318.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CTTNBP2NL	ENST00000271277.11	c.*2446G>A		3_prime_UTR_variant	6/6	1	NM_018704.3	ENSP00000271277.6
CTTNBP2NL	ENST00000607039.1	n.557+2484G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31769 AN: 152040 Hom.: 4077 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.188

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.224

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.209 AC: 31772 AN: 152158 Hom.: 4077 Cov.: 32 AF XY: 0.218 AC XY: 16232 AN XY: 74380

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.552

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.223

Alfa AF: 0.215 Hom.: 835

Bravo AF: 0.212

Asia WGS AF: 0.391 AC: 1356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	17
DANN	Benign	0.88

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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

Other links and lift over

dbSNP: rs3762332; hg19: chr1-113002480;