dbSNP rs3795821: CTTNBP2NL:c.*531A>G (chr1-112457943-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.282

Publications

8 publications found

Variant links:

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 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
CTTNBP2NL	NM_018704.3 link	c.*531A>G	3_prime_UTR_variant	Exon 6 of 6	ENST00000271277.11	NP_061174.1	Q9P2B4
CTTNBP2NL	XM_011541781.3 link	c.*531A>G	3_prime_UTR_variant	Exon 6 of 6		XP_011540083.1	Q9P2B4
CTTNBP2NL	XM_017001806.2 link	c.*531A>G	3_prime_UTR_variant	Exon 6 of 6		XP_016857295.1	Q9P2B4
CTTNBP2NL	XM_047425362.1 link	c.*531A>G	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 link	c.*531A>G		3_prime_UTR_variant	Exon 6 of 6	1	NM_018704.3	ENSP00000271277.6		Q9P2B4
CTTNBP2NL	ENST00000607039.1 link	n.557+569A>G		intron_variant	Intron 1 of 1	1

Frequencies

GnomAD3 genomes

AF:

0.209

AC:

31732

AN:

152036

Hom.:

4069

Cov.:

show subpopulations

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.:

Cov.:

AF XY:

0.199

AC XY:

188

AN XY:

946

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.301

AC:

AN:

156

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AF:

0.125

AC:

AN:

European-Finnish (FIN)

AF:

0.259

AC:

113

AN:

436

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.152

AC:

146

AN:

958

Other (OTH)

AF:

0.0769

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.209

AC:

31735

AN:

152154

Hom.:

4069

Cov.:

AF XY:

0.218

AC XY:

16206

AN XY:

74370

show subpopulations

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.207

AC:

14073

AN:

68002

Other (OTH)

AF:

0.223

AC:

469

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1245

2491

3736

4982

6227

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

344

688

1032

1376

1720

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

8.9

(source)

DANN

Benign

0.78

PhyloP100

0.28

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over