rs7507634

Variant names:

• chr19-10325886-C-T
• rs7507634
• NM_133452.3:c.757-2320G>A

Variant summary

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

The NM_133452.3(RAVER1):​c.757-2320G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0904 in 152,072 control chromosomes in the GnomAD database, including 854 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 0.090 (854 hom., cov: 32)
• Consequence: RAVER1 NM_133452.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.970
• Publications: 5 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAVER1	NM_133452.3	c.757-2320G>A		intron_variant	Intron 3 of 12	ENST00000617231.5	NP_597709.3
RAVER1	NM_001366174.1	c.757-2320G>A		intron_variant	Intron 3 of 13		NP_001353103.1
RAVER1	XM_047438141.1	c.757-2320G>A		intron_variant	Intron 3 of 9		XP_047294097.1
RAVER1	XM_047438142.1	c.757-2320G>A		intron_variant	Intron 3 of 7		XP_047294098.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAVER1	ENST00000617231.5	c.757-2320G>A		intron_variant	Intron 3 of 12	5	NM_133452.3	ENSP00000482277.1
RAVER1	ENST00000592208.5	n.694-2320G>A		intron_variant	Intron 2 of 9	1
RAVER1	ENST00000591969.2	n.*392-2320G>A		intron_variant	Intron 3 of 3	3		ENSP00000465753.2

Frequencies

GnomAD3 genomes AF: 0.0905 AC: 13745 AN: 151954 Hom.: 853 Cov.: 32

Gnomad AFR AF: 0.0226

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.0759

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0591

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.0948

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

GnomAD4 genome AF: 0.0904 AC: 13745 AN: 152072 Hom.: 854 Cov.: 32 AF XY: 0.0925 AC XY: 6879 AN XY: 74340

African (AFR) AF: 0.0225 AC: 935 AN: 41472

American (AMR) AF: 0.175 AC: 2676 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.0759 AC: 263 AN: 3466

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5182

South Asian (SAS) AF: 0.0595 AC: 287 AN: 4822

European-Finnish (FIN) AF: 0.160 AC: 1693 AN: 10564

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7544 AN: 68000

Other (OTH) AF: 0.0934 AC: 197 AN: 2110

Alfa AF: 0.0944 Hom.: 713

Bravo AF: 0.0909

Asia WGS AF: 0.0320 AC: 112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.51
PhyloP100		0.97
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: rs7507634; hg19: chr19-10436562;