chr1-64827766-A-T

Variant names:

• chr1-64827766-A-T
• rs1333739
• NM_001366165.2:c.1930-3073A>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.1930-3073A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.619 in 152,164 control chromosomes in the GnomAD database, including 32,003 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 0.62 (32003 hom., cov: 33)
• Consequence: RAVER2 NM_001366165.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.733
• Publications: 2 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.904 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAVER2	NM_001366165.2	c.1930-3073A>T		intron_variant	Intron 11 of 11	ENST00000294428.8	NP_001353094.1
RAVER2	NM_018211.4	c.1891-3073A>T		intron_variant	Intron 11 of 11		NP_060681.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAVER2	ENST00000294428.8	c.1930-3073A>T		intron_variant	Intron 11 of 11	5	NM_001366165.2	ENSP00000294428.3
RAVER2	ENST00000371072.8	c.1891-3073A>T		intron_variant	Intron 11 of 11	1		ENSP00000360112.4

Frequencies

GnomAD3 genomes AF: 0.619 AC: 94045 AN: 152046 Hom.: 31940 Cov.: 33

Gnomad AFR AF: 0.882

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.642

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.926

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.608

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.619 AC: 94175 AN: 152164 Hom.: 32003 Cov.: 33 AF XY: 0.628 AC XY: 46729 AN XY: 74388

African (AFR) AF: 0.883 AC: 36671 AN: 41546

American (AMR) AF: 0.642 AC: 9823 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.542 AC: 1883 AN: 3472

East Asian (EAS) AF: 0.926 AC: 4800 AN: 5184

South Asian (SAS) AF: 0.508 AC: 2450 AN: 4822

European-Finnish (FIN) AF: 0.608 AC: 6430 AN: 10576

Middle Eastern (MID) AF: 0.390 AC: 114 AN: 292

European-Non Finnish (NFE) AF: 0.447 AC: 30364 AN: 67954

Other (OTH) AF: 0.590 AC: 1248 AN: 2116

Alfa AF: 0.559 Hom.: 3193

Bravo AF: 0.637

Asia WGS AF: 0.746 AC: 2592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.36
DANN	Benign	0.85
PhyloP100		-0.73
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: rs1333739; hg19: chr1-65293449;