Variant rs401681 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_030782.5(CLPTM1L):c.1316-153G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.472 in 151958 control chromosomes in the gnomAD Genomes database, including 17526 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 0.47 ( 17526 hom., cov: 34)

Consequence

CLPTM1L
NM_030782.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.26

Links

CLPTM1L (HGNC:24308):

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BA1

GnomAd highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
CLPTM1L	NM_030782.5 linkuse as main transcript	c.1316-153G>A	intron_variant	ENST00000320895.10
CLPTM1L	XM_011514144.3 linkuse as main transcript	c.1313-153G>A	intron_variant
CLPTM1L	XM_024446222.2 linkuse as main transcript	c.782-153G>A	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLPTM1L	ENST00000320895.10 linkuse as main transcript	c.1316-153G>A		intron_variant		1	NM_030782.5	P1	Q96KA5-1

Frequencies

GnomAD3 genomes

AF:

0.472

AC:

71708

AN:

151958

Hom.:

17526

Cov.:

show subpopulations

Gnomad AFR

AF:

0.593

Gnomad AMI

AF:

0.474

Gnomad AMR

AF:

0.433

Gnomad ASJ

AF:

0.449

Gnomad EAS

AF:

0.319

Gnomad SAS

AF:

0.214

Gnomad FIN

AF:

0.494

Gnomad MID

AF:

0.440

Gnomad NFE

AF:

0.435

Gnomad OTH

AF:

0.452

GnomAD4 exome

AF:

0.414

AC:

228381

AN:

552278

Hom.:

49558

AF XY:

0.402

AC XY:

117952

AN XY:

293754

show subpopulations

Gnomad4 AFR exome

AF:

0.593

Gnomad4 AMR exome

AF:

0.406

Gnomad4 ASJ exome

AF:

0.434

Gnomad4 EAS exome

AF:

0.331

Gnomad4 SAS exome

AF:

0.205

Gnomad4 FIN exome

AF:

0.492

Gnomad4 NFE exome

AF:

0.436

Gnomad4 OTH exome

AF:

0.433

Alfa

AF:

0.433

Hom.:

17929

Bravo

AF:

0.480

Asia WGS

AF:

0.290

AC:

1009

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

Cadd

Benign

0.12

Dann

Benign

0.39

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

LitVar

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

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over