1-112457943-A-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018704.3(CTTNBP2NL):​c.*531A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 153,842 control chromosomes in the GnomAD database, including 4,110 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 (4069 hom., cov: 32)
  • Exomes 𝑓: 0.19 (41 hom.)
• Consequence: CTTNBP2NL NM_018704.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282
• 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.534 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CTTNBP2NL	NM_018704.3	MANE Select	c.*531A>G		3_prime_UTR	Exon 6 of 6	NP_061174.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CTTNBP2NL	ENST00000271277.11	TSL:1 MANE Select	c.*531A>G		3_prime_UTR	Exon 6 of 6	ENSP00000271277.6
	CTTNBP2NL	ENST00000607039.1	TSL:1	n.557+569A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31732 AN: 152036 Hom.: 4069 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.224

GnomAD4 exome AF: 0.194 AC: 327 AN: 1688 Hom.: 41 Cov.: 0 AF XY: 0.199 AC XY: 188 AN XY: 946

African (AFR) AF: 0.00 AC: 0 AN: 4

American (AMR) AF: 0.301 AC: 47 AN: 156

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 4 AN: 8

East Asian (EAS) AF: 0.500 AC: 5 AN: 10

South Asian (SAS) AF: 0.125 AC: 8 AN: 64

European-Finnish (FIN) AF: 0.259 AC: 113 AN: 436

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.152 AC: 146 AN: 958

Other (OTH) AF: 0.0769 AC: 4 AN: 52

GnomAD4 genome AF: 0.209 AC: 31735 AN: 152154 Hom.: 4069 Cov.: 32 AF XY: 0.218 AC XY: 16206 AN XY: 74370

African (AFR) AF: 0.105 AC: 4380 AN: 41560

American (AMR) AF: 0.308 AC: 4700 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 884 AN: 3470

East Asian (EAS) AF: 0.551 AC: 2843 AN: 5156

South Asian (SAS) AF: 0.229 AC: 1102 AN: 4812

European-Finnish (FIN) AF: 0.284 AC: 3004 AN: 10568

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.207 AC: 14073 AN: 68002

Other (OTH) AF: 0.223 AC: 469 AN: 2106

Alfa AF: 0.205 Hom.: 3695

Bravo AF: 0.212

Asia WGS AF: 0.391 AC: 1357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.9
DANN	Benign	0.78
PhyloP100		0.28
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: rs3795821; hg19: chr1-113000565;