1-64833108-A-T

Position:

• chr1-64833108-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001366165.2(RAVER2):​c.*2123A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 178,872 control chromosomes in the GnomAD database, including 25,746 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 0.51 (23084 hom., cov: 32)
  • Exomes 𝑓: 0.41 (2662 hom.)
• Consequence: RAVER2 NM_001366165.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.122

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.833 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RAVER2	NM_001366165.2	c.*2123A>T		3_prime_UTR_variant	12/12	ENST00000294428.8
RAVER2	NM_018211.4	c.*2123A>T		3_prime_UTR_variant	12/12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RAVER2	ENST00000294428.8	c.*2123A>T		3_prime_UTR_variant	12/12	5	NM_001366165.2	A2
RAVER2	ENST00000371072.8	c.*2123A>T		3_prime_UTR_variant	12/12	1		P2

Frequencies

GnomAD3 genomes AF: 0.511 AC: 76940 AN: 150620 Hom.: 23029 Cov.: 32

Gnomad AFR AF: 0.841

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.617

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.470

GnomAD4 exome AF: 0.411 AC: 11568 AN: 28140 Hom.: 2662 Cov.: 0 AF XY: 0.405 AC XY: 5222 AN XY: 12898

Gnomad4 AFR exome AF: 0.837

Gnomad4 AMR exome AF: 0.412

Gnomad4 ASJ exome AF: 0.447

Gnomad4 EAS exome AF: 0.572

Gnomad4 SAS exome AF: 0.373

Gnomad4 FIN exome AF: 0.389

Gnomad4 NFE exome AF: 0.329

Gnomad4 OTH exome AF: 0.404

GnomAD4 genome AF: 0.511 AC: 77058 AN: 150732 Hom.: 23084 Cov.: 32 AF XY: 0.510 AC XY: 37544 AN XY: 73628

Gnomad4 AFR AF: 0.841

Gnomad4 AMR AF: 0.417

Gnomad4 ASJ AF: 0.472

Gnomad4 EAS AF: 0.617

Gnomad4 SAS AF: 0.357

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.354

Gnomad4 OTH AF: 0.474

Alfa AF: 0.464 Hom.: 2326

Bravo AF: 0.524

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.0
DANN	Benign	0.83

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

Publications

LitVar

Other links and lift over

dbSNP: rs2780889; hg19: chr1-65298791;