rs11083758

chr19-45043803-C-G

Variant summary

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

The NM_007056.3(CLASRP):c.99+3492C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.539 in 151,950 control chromosomes in the GnomAD database, including 22,419 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 0.54 (22419 hom., cov: 31)
• Consequence: CLASRP NM_007056.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.340

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLASRP	NM_007056.3	c.99+3492C>G		intron_variant		ENST00000221455.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLASRP	ENST00000221455.8	c.99+3492C>G		intron_variant		1	NM_007056.3	P2

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81864 AN: 151832 Hom.: 22397 Cov.: 31

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.539 AC: 81935 AN: 151950 Hom.: 22419 Cov.: 31 AF XY: 0.534 AC XY: 39638 AN XY: 74262

Gnomad4 AFR AF: 0.621

Gnomad4 AMR AF: 0.476

Gnomad4 ASJ AF: 0.483

Gnomad4 EAS AF: 0.408

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.507

Gnomad4 NFE AF: 0.532

Gnomad4 OTH AF: 0.539

Alfa AF: 0.537 Hom.: 2813

Bravo AF: 0.542

Asia WGS AF: 0.440 AC: 1534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.38
Dann	Benign	0.43

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: rs11083758; hg19: chr19-45547061;