Variant rs7257610 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001294.4(CLPTM1):c.794-9G>A variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0479 in 1,604,814 control chromosomes in the GnomAD database, including 2,193 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 0.064 ( 386 hom., cov: 34)

Exomes 𝑓: 0.046 ( 1807 hom. )

Consequence

CLPTM1
NM_001294.4 splice_polypyrimidine_tract, intron

Scores

Splicing: ADA: 0.0003402

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.53

Variant links:

Genes affected

CLPTM1 (HGNC:2087): (CLPTM1 regulator of GABA type A receptor forward trafficking) Predicted to be involved in regulation of T cell differentiation in thymus. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

CLPTM1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.111 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
CLPTM1	NM_001294.4 linkuse as main transcript	c.794-9G>A	splice_polypyrimidine_tract_variant, intron_variant	ENST00000337392.10
CLPTM1	NM_001282175.2 linkuse as main transcript	c.752-9G>A	splice_polypyrimidine_tract_variant, intron_variant
CLPTM1	NM_001282176.2 linkuse as main transcript	c.488-9G>A	splice_polypyrimidine_tract_variant, intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLPTM1	ENST00000337392.10 linkuse as main transcript	c.794-9G>A		splice_polypyrimidine_tract_variant, intron_variant		1	NM_001294.4	P1	O96005-1

Frequencies

GnomAD3 genomes

AF:

0.0639

AC:

9728

AN:

152166

Hom.:

385

Cov.:

show subpopulations

Gnomad AFR

AF:

0.114

Gnomad AMI

AF:

0.133

Gnomad AMR

AF:

0.0389

Gnomad ASJ

AF:

0.0516

Gnomad EAS

AF:

0.0235

Gnomad SAS

AF:

0.0859

Gnomad FIN

AF:

0.0403

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0444

Gnomad OTH

AF:

0.0569

GnomAD3 exomes

AF:

0.0487

AC:

12062

AN:

247882

Hom.:

370

AF XY:

0.0499

AC XY:

6688

AN XY:

133936

show subpopulations

Gnomad AFR exome

AF:

0.117

Gnomad AMR exome

AF:

0.0249

Gnomad ASJ exome

AF:

0.0534

Gnomad EAS exome

AF:

0.0229

Gnomad SAS exome

AF:

0.0711

Gnomad FIN exome

AF:

0.0379

Gnomad NFE exome

AF:

0.0459

Gnomad OTH exome

AF:

0.0491

GnomAD4 exome

AF:

0.0462

AC:

67067

AN:

1452530

Hom.:

1807

Cov.:

AF XY:

0.0471

AC XY:

33939

AN XY:

721096

show subpopulations

Gnomad4 AFR exome

AF:

0.118

Gnomad4 AMR exome

AF:

0.0261

Gnomad4 ASJ exome

AF:

0.0543

Gnomad4 EAS exome

AF:

0.0149

Gnomad4 SAS exome

AF:

0.0730

Gnomad4 FIN exome

AF:

0.0361

Gnomad4 NFE exome

AF:

0.0439

Gnomad4 OTH exome

AF:

0.0497

GnomAD4 genome

AF:

0.0640

AC:

9741

AN:

152284

Hom.:

386

Cov.:

AF XY:

0.0630

AC XY:

4692

AN XY:

74470

show subpopulations

Gnomad4 AFR

AF:

0.114

Gnomad4 AMR

AF:

0.0387

Gnomad4 ASJ

AF:

0.0516

Gnomad4 EAS

AF:

0.0235

Gnomad4 SAS

AF:

0.0857

Gnomad4 FIN

AF:

0.0403

Gnomad4 NFE

AF:

0.0444

Gnomad4 OTH

AF:

0.0563

Alfa

AF:

0.0510

Hom.:

298

Bravo

AF:

0.0650

Asia WGS

AF:

0.0400

AC:

142

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.14

DANN

Benign

0.81

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00034

dbscSNV1_RF

Benign

0.036

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over