1-112457943-A-T

Variant names:

• chr1-112457943-A-T
• rs3795821
• NM_018704.3:c.*531A>T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_018704.3(CTTNBP2NL):​c.*531A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: CTTNBP2NL NM_018704.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282

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 Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CTTNBP2NL	NM_018704.3	c.*531A>T		3_prime_UTR_variant	Exon 6 of 6	ENST00000271277.11	NP_061174.1
CTTNBP2NL	XM_011541781.3	c.*531A>T		3_prime_UTR_variant	Exon 6 of 6		XP_011540083.1
CTTNBP2NL	XM_017001806.2	c.*531A>T		3_prime_UTR_variant	Exon 6 of 6		XP_016857295.1
CTTNBP2NL	XM_047425362.1	c.*531A>T		3_prime_UTR_variant	Exon 6 of 6		XP_047281318.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CTTNBP2NL	ENST00000271277.11	c.*531A>T		3_prime_UTR_variant	Exon 6 of 6	1	NM_018704.3	ENSP00000271277.6
CTTNBP2NL	ENST00000607039.1	n.557+569A>T		intron_variant	Intron 1 of 1	1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.4
DANN	Benign	0.70

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs3795821; hg19: chr1-113000565;