rs3786507

Positions:

• chr19-45044997-G-A
• chr19-45044997-G-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+4686G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.673 in 152,102 control chromosomes in the GnomAD database, including 35,323 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 0.67 (35323 hom., cov: 32)
• Consequence: CLASRP NM_007056.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.177

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 (EAS) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLASRP	NM_007056.3	c.99+4686G>A		intron_variant		ENST00000221455.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLASRP	ENST00000221455.8	c.99+4686G>A		intron_variant		1	NM_007056.3	P2

Frequencies

GnomAD3 genomes AF: 0.672 AC: 102174 AN: 151986 Hom.: 35268 Cov.: 32

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.644

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.903

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.659

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

GnomAD4 genome AF: 0.673 AC: 102289 AN: 152102 Hom.: 35323 Cov.: 32 AF XY: 0.676 AC XY: 50228 AN XY: 74344

Gnomad4 AFR AF: 0.815

Gnomad4 AMR AF: 0.644

Gnomad4 ASJ AF: 0.578

Gnomad4 EAS AF: 0.904

Gnomad4 SAS AF: 0.638

Gnomad4 FIN AF: 0.628

Gnomad4 NFE AF: 0.591

Gnomad4 OTH AF: 0.664

Alfa AF: 0.602 Hom.: 37505

Bravo AF: 0.683

Asia WGS AF: 0.779 AC: 2709 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	1.2
DANN	Benign	0.44

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: rs3786507; hg19: chr19-45548255;