NM_007056.3:c.99+3492C>G

Variant names:

• chr19-45043803-C-G
• rs11083758
• NM_007056.3:c.99+3492C>G

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+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
• Publications: 4 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.614 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLASRP	NM_007056.3	MANE Select	c.99+3492C>G		intron	N/A	NP_008987.2
	CLASRP	NM_001278439.2		c.99+3492C>G		intron	N/A	NP_001265368.1
	CLASRP	NR_103529.2		n.192+3492C>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLASRP	ENST00000221455.8	TSL:1 MANE Select	c.99+3492C>G		intron	N/A	ENSP00000221455.3
	CLASRP	ENST00000391952.7	TSL:1	n.99+3492C>G		intron	N/A	ENSP00000375814.2
	CLASRP	ENST00000587112.1	TSL:1	n.42+3492C>G		intron	N/A	ENSP00000466371.1

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

African (AFR) AF: 0.621 AC: 25715 AN: 41434

American (AMR) AF: 0.476 AC: 7254 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.483 AC: 1676 AN: 3472

East Asian (EAS) AF: 0.408 AC: 2108 AN: 5164

South Asian (SAS) AF: 0.405 AC: 1951 AN: 4822

European-Finnish (FIN) AF: 0.507 AC: 5347 AN: 10556

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.532 AC: 36120 AN: 67942

Other (OTH) AF: 0.539 AC: 1136 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.38
DANN	Benign	0.43
PhyloP100		-0.34
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: rs11083758; hg19: chr19-45547061;