rs3786507

Variant names:

• chr19-45044997-G-A
• rs3786507
• NM_007056.3:c.99+4686G>A

Your query was ambiguous. Multiple possible variants found:

• chr19-45044997-G-A
• chr19-45044997-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 14 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007056.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLASRP	NM_007056.3	MANE Select	c.99+4686G>A		intron	N/A	NP_008987.2	Q8N2M8-1
	CLASRP	NM_001278439.2		c.99+4686G>A		intron	N/A	NP_001265368.1	Q8N2M8-4
	CLASRP	NR_103529.2		n.192+4686G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLASRP	ENST00000221455.8	TSL:1 MANE Select	c.99+4686G>A		intron	N/A	ENSP00000221455.3	Q8N2M8-1
	CLASRP	ENST00000391952.7	TSL:1	n.99+4686G>A		intron	N/A	ENSP00000375814.2	Q8N2M8-3
	CLASRP	ENST00000587112.1	TSL:1	n.42+4686G>A		intron	N/A	ENSP00000466371.1	K7EM61

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

African (AFR) AF: 0.815 AC: 33842 AN: 41516

American (AMR) AF: 0.644 AC: 9830 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2005 AN: 3468

East Asian (EAS) AF: 0.904 AC: 4680 AN: 5178

South Asian (SAS) AF: 0.638 AC: 3069 AN: 4814

European-Finnish (FIN) AF: 0.628 AC: 6640 AN: 10574

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.591 AC: 40148 AN: 67976

Other (OTH) AF: 0.664 AC: 1403 AN: 2114

Alfa AF: 0.615 Hom.: 54593

Bravo AF: 0.683

Asia WGS AF: 0.779 AC: 2709 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.44
PhyloP100		-0.18
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3786507; hg19: chr19-45548255;