19-45040529-C-T

Position:

• chr19-45040529-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0990

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 (HGNC:):

ACMG classification

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	Protein	UniProt
CLASRP	NM_007056.3	c.99+218C>T		intron_variant		ENST00000221455.8	NP_008987.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CLASRP	ENST00000221455.8	c.99+218C>T		intron_variant		1	NM_007056.3	ENSP00000221455.3

Frequencies

GnomAD3 genomes AF: 0.474 AC: 71930 AN: 151782 Hom.: 17553 Cov.: 32

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.: 3 AF XY: 0.494 AC XY: 71604 AN XY: 144808

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.: 32 AF XY: 0.469 AC XY: 34839 AN XY: 74226

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

Other links and lift over

dbSNP: rs1560725; hg19: chr19-45543787;