Variant rs9914733 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_030665.4(RAI1):c.-148-5206C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 152,014 control chromosomes in the GnomAD database, including 4,985 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 0.25 ( 4985 hom., cov: 31)

Consequence

RAI1
NM_030665.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.509

Variant links:

Genes affected

RAI1 (HGNC:9834): (retinoic acid induced 1) This gene is located within the Smith-Magenis syndrome region on chromosome 17. It is highly similar to its mouse counterpart and is expressed at high levels mainly in neuronal tissues. The protein encoded by this gene includes a polymorphic polyglutamine tract in the N-terminal domain. Expression of the mouse counterpart in neurons is induced by retinoic acid. This gene is associated with both the severity of the phenotype and the response to medication in schizophrenic patients. [provided by RefSeq, Jul 2008]

RAI1 links:

LOC124903943 (HGNC:):

LOC124903943 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RAI1	NM_030665.4 linkuse as main transcript	c.-148-5206C>G		intron_variant		ENST00000353383.6	NP_109590.3
LOC124903943	XR_007065650.1 linkuse as main transcript	n.3499G>C		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RAI1	ENST00000353383.6 linkuse as main transcript	c.-148-5206C>G		intron_variant		1	NM_030665.4	ENSP00000323074	P1	Q7Z5J4-1
RAI1	ENST00000471135.2 linkuse as main transcript	c.-148-5206C>G		intron_variant		3		ENSP00000463607

Frequencies

GnomAD3 genomes

AF:

0.251

AC:

38149

AN:

151896

Hom.:

4979

Cov.:

show subpopulations

Gnomad AFR

AF:

0.293

Gnomad AMI

AF:

0.115

Gnomad AMR

AF:

0.264

Gnomad ASJ

AF:

0.217

Gnomad EAS

AF:

0.351

Gnomad SAS

AF:

0.163

Gnomad FIN

AF:

0.243

Gnomad MID

AF:

0.199

Gnomad NFE

AF:

0.226

Gnomad OTH

AF:

0.266

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

GnomAD4 genome

AF:

0.251

AC:

38184

AN:

152014

Hom.:

4985

Cov.:

AF XY:

0.251

AC XY:

18647

AN XY:

74306

show subpopulations

Gnomad4 AFR

AF:

0.293

Gnomad4 AMR

AF:

0.265

Gnomad4 ASJ

AF:

0.217

Gnomad4 EAS

AF:

0.351

Gnomad4 SAS

AF:

0.163

Gnomad4 FIN

AF:

0.243

Gnomad4 NFE

AF:

0.226

Gnomad4 OTH

AF:

0.270

Alfa

AF:

0.227

Hom.:

520

Bravo

AF:

0.261

Asia WGS

AF:

0.284

AC:

987

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

DANN

Benign

0.75

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over