rs3762332

Variant names:

• chr1-112459858-G-A
• rs3762332
• NM_018704.3:c.*2446G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 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 -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018704.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CTTNBP2NL	NM_018704.3	MANE Select	c.*2446G>A		3_prime_UTR	Exon 6 of 6	NP_061174.1	Q9P2B4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CTTNBP2NL	ENST00000271277.11	TSL:1 MANE Select	c.*2446G>A		3_prime_UTR	Exon 6 of 6	ENSP00000271277.6	Q9P2B4
	CTTNBP2NL	ENST00000607039.1	TSL:1	n.557+2484G>A		intron	N/A
	CTTNBP2NL	ENST00000862867.1		c.*2446G>A		3_prime_UTR	Exon 7 of 7	ENSP00000532926.1

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

African (AFR) AC: 0 AN: 0

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) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.105 AC: 4370 AN: 41528

American (AMR) AF: 0.308 AC: 4714 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 885 AN: 3472

East Asian (EAS) AF: 0.552 AC: 2851 AN: 5164

South Asian (SAS) AF: 0.229 AC: 1105 AN: 4830

European-Finnish (FIN) AF: 0.285 AC: 3013 AN: 10572

Middle Eastern (MID) AF: 0.199 AC: 58 AN: 292

European-Non Finnish (NFE) AF: 0.207 AC: 14083 AN: 67982

Other (OTH) AF: 0.223 AC: 472 AN: 2114

Alfa AF: 0.215 Hom.: 1352

Bravo AF: 0.212

Asia WGS AF: 0.391 AC: 1356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	17
DANN	Benign	0.88
PhyloP100		3.4
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3762332; hg19: chr1-113002480;