rs2889490

chr19-45047149-A-G

Variant summary

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

The NM_007056.3(CLASRP):c.100-4922A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 151,936 control chromosomes in the GnomAD database, including 16,144 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 0.46 (16144 hom., cov: 31)
• Consequence: CLASRP NM_007056.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.233

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.505 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLASRP	NM_007056.3	c.100-4922A>G		intron_variant		ENST00000221455.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLASRP	ENST00000221455.8	c.100-4922A>G		intron_variant		1	NM_007056.3	P2

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69283 AN: 151818 Hom.: 16142 Cov.: 31

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.473

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.456 AC: 69309 AN: 151936 Hom.: 16144 Cov.: 31 AF XY: 0.454 AC XY: 33694 AN XY: 74224

Gnomad4 AFR AF: 0.373

Gnomad4 AMR AF: 0.446

Gnomad4 ASJ AF: 0.464

Gnomad4 EAS AF: 0.413

Gnomad4 SAS AF: 0.386

Gnomad4 FIN AF: 0.495

Gnomad4 NFE AF: 0.510

Gnomad4 OTH AF: 0.476

Alfa AF: 0.471 Hom.: 3329

Bravo AF: 0.449

Asia WGS AF: 0.423 AC: 1474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	3.6
Dann	Benign	0.71

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: rs2889490; hg19: chr19-45550407;