rs3818729

Variant names:

• chr1-112449240-G-A
• rs3818729
• NM_018704.3:c.330+68G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-112449240-G-A
• chr1-112449240-G-C
• chr1-112449240-G-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_018704.3(CTTNBP2NL):​c.330+68G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000121 in 741,226 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 29)
  • Exomes 𝑓: 0.000012 (0 hom.)
• Consequence: CTTNBP2NL NM_018704.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.326
• Publications: 0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CTTNBP2NL	NM_018704.3	c.330+68G>A		intron_variant	Intron 4 of 5	ENST00000271277.11	NP_061174.1
CTTNBP2NL	XM_011541781.3	c.330+68G>A		intron_variant	Intron 4 of 5		XP_011540083.1
CTTNBP2NL	XM_017001806.2	c.330+68G>A		intron_variant	Intron 4 of 5		XP_016857295.1
CTTNBP2NL	XM_047425362.1	c.330+68G>A		intron_variant	Intron 4 of 5		XP_047281318.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CTTNBP2NL	ENST00000271277.11	c.330+68G>A		intron_variant	Intron 4 of 5	1	NM_018704.3	ENSP00000271277.6
CTTNBP2NL	ENST00000441739.1	c.330+68G>A		intron_variant	Intron 4 of 5	3		ENSP00000390976.1

Frequencies

GnomAD3 genomes Cov.: 29

GnomAD4 exome AF: 0.0000121 AC: 9 AN: 741226 Hom.: 0 AF XY: 0.0000238 AC XY: 9 AN XY: 378274

African (AFR) AF: 0.00 AC: 0 AN: 18700

American (AMR) AF: 0.00 AC: 0 AN: 25320

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 17120

East Asian (EAS) AF: 0.00 AC: 0 AN: 33242

South Asian (SAS) AF: 0.000167 AC: 9 AN: 53788

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 45882

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3194

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 508236

Other (OTH) AF: 0.00 AC: 0 AN: 35744

GnomAD4 genome Cov.: 29

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.3
DANN	Benign	0.73
PhyloP100		0.33

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: rs3818729; hg19: chr1-112991862;