rs1444038605

Variant names:

• chr19-10320917-C-A
• rs1444038605
• NM_133452.3:c.1508G>T

Your query was ambiguous. Multiple possible variants found:

• chr19-10320917-C-A
• chr19-10320917-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_133452.3(RAVER1):​c.1508G>T​(p.Arg503Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R503Q) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: RAVER1 NM_133452.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.03

Genes affected

RAVER1 (HGNC:30296): (ribonucleoprotein, PTB binding 1) Enables RNA binding activity. Predicted to be involved in regulation of alternative mRNA splicing, via spliceosome. Predicted to be located in cytoplasm. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000267303 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAVER1	NM_133452.3	c.1508G>T	p.Arg503Leu	missense_variant	Exon 9 of 13	ENST00000617231.5	NP_597709.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAVER1	ENST00000617231.5	c.1508G>T	p.Arg503Leu	missense_variant	Exon 9 of 13	5	NM_133452.3	ENSP00000482277.1
ENSG00000267303	ENST00000586529.1	n.-239G>T		upstream_gene_variant		5		ENSP00000467814.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1348460 Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0 AN XY: 662438

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.19	D
BayesDel_noAF	Uncertain	0.040
CADD	Pathogenic	27
DANN	Uncertain	1.0
DEOGEN2	Benign	0.13	.;T;T
Eigen	Uncertain	0.36
Eigen_PC	Uncertain	0.34
FATHMM_MKL	Uncertain	0.80	D
LIST_S2	Uncertain	0.89	D;.;D
M_CAP	Uncertain	0.15	D
MetaRNN	Uncertain	0.69	D;D;D
MetaSVM	Uncertain	-0.036	T
PrimateAI	Uncertain	0.60	T
PROVEAN	Uncertain	-2.9	.;D;.
REVEL	Uncertain	0.53
Sift	Uncertain	0.0060	.;D;.
Sift4G	Benign	0.14	T;T;T
Polyphen		0.98	.;D;D
Vest4		0.72
MutPred		0.43		.;Gain of glycosylation at P516 (P = 0.0748);Gain of glycosylation at P516 (P = 0.0748);
MVP		0.79
MPC		0.41
ClinPred		0.86	D
GERP RS		3.3
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.8
gMVP		0.35

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs1444038605; hg19: chr19-10431593;