1-64827272-C-T

Variant names:

• chr1-64827272-C-T
• rs2780814
• NM_001366165.2:c.1930-3567C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001366165.2(RAVER2):​c.1930-3567C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 151,882 control chromosomes in the GnomAD database, including 20,555 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 0.48 (20555 hom., cov: 31)
• Consequence: RAVER2 NM_001366165.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 3 publications found

Genes affected

RAVER2 (HGNC:25577): (ribonucleoprotein, PTB binding 2) 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001366165.2. 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
	RAVER2	NM_001366165.2	MANE Select	c.1930-3567C>T		intron	N/A	NP_001353094.1
	RAVER2	NM_018211.4		c.1891-3567C>T		intron	N/A	NP_060681.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RAVER2	ENST00000294428.8	TSL:5 MANE Select	c.1930-3567C>T		intron	N/A	ENSP00000294428.3
	RAVER2	ENST00000371072.8	TSL:1	c.1891-3567C>T		intron	N/A	ENSP00000360112.4

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73526 AN: 151764 Hom.: 20498 Cov.: 31

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.590

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.485 AC: 73647 AN: 151882 Hom.: 20555 Cov.: 31 AF XY: 0.491 AC XY: 36430 AN XY: 74224

African (AFR) AF: 0.776 AC: 32131 AN: 41428

American (AMR) AF: 0.466 AC: 7113 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 1279 AN: 3466

East Asian (EAS) AF: 0.590 AC: 3044 AN: 5160

South Asian (SAS) AF: 0.329 AC: 1578 AN: 4794

European-Finnish (FIN) AF: 0.439 AC: 4617 AN: 10528

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.331 AC: 22467 AN: 67928

Other (OTH) AF: 0.454 AC: 956 AN: 2106

Alfa AF: 0.405 Hom.: 1716

Bravo AF: 0.503

Asia WGS AF: 0.503 AC: 1748 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.59
DANN	Benign	0.31
PhyloP100		-1.5
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: rs2780814; hg19: chr1-65292955;