Variant 19-45040529-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_007056.3(CLASRP):c.99+218C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.491 in 423,822 control chromosomes in the GnomAD database, including 52,643 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 ( 17555 hom., cov: 32)

Exomes 𝑓: 0.50 ( 35088 hom. )

Consequence

CLASRP
NM_007056.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0990

Variant links:

Genes affected

CLASRP (HGNC:17731): (CLK4 associating serine/arginine rich protein) Predicted to be involved in RNA splicing and mRNA processing. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

CLASRP 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=-0.81).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLASRP	NM_007056.3 linkuse as main transcript	c.99+218C>T		intron_variant		ENST00000221455.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLASRP	ENST00000221455.8 linkuse as main transcript	c.99+218C>T		intron_variant		1	NM_007056.3	P2

Frequencies

GnomAD3 genomes

AF:

0.474

AC:

71930

AN:

151782

Hom.:

17553

Cov.:

show subpopulations

Gnomad AFR

AF:

0.363

Gnomad AMI

AF:

0.515

Gnomad AMR

AF:

0.461

Gnomad ASJ

AF:

0.482

Gnomad EAS

AF:

0.425

Gnomad SAS

AF:

0.395

Gnomad FIN

AF:

0.494

Gnomad MID

AF:

0.538

Gnomad NFE

AF:

0.548

Gnomad OTH

AF:

0.496

GnomAD4 exome

AF:

0.501

AC:

136249

AN:

271922

Hom.:

35088

Cov.:

AF XY:

0.494

AC XY:

71604

AN XY:

144808

show subpopulations

Gnomad4 AFR exome

AF:

0.366

Gnomad4 AMR exome

AF:

0.450

Gnomad4 ASJ exome

AF:

0.481

Gnomad4 EAS exome

AF:

0.438

Gnomad4 SAS exome

AF:

0.386

Gnomad4 FIN exome

AF:

0.498

Gnomad4 NFE exome

AF:

0.546

Gnomad4 OTH exome

AF:

0.504

GnomAD4 genome

AF:

0.474

AC:

71950

AN:

151900

Hom.:

17555

Cov.:

AF XY:

0.469

AC XY:

34839

AN XY:

74226

show subpopulations

Gnomad4 AFR

AF:

0.363

Gnomad4 AMR

AF:

0.460

Gnomad4 ASJ

AF:

0.482

Gnomad4 EAS

AF:

0.424

Gnomad4 SAS

AF:

0.395

Gnomad4 FIN

AF:

0.494

Gnomad4 NFE

AF:

0.548

Gnomad4 OTH

AF:

0.498

Alfa

AF:

0.529

Hom.:

29128

Bravo

AF:

0.467

Asia WGS

AF:

0.428

AC:

1491

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

Cadd

Benign

2.9

Dann

Benign

0.75

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over