rs2284390

Variant summary

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

The NM_016732.3(RALY):​c.-9-2282G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0991 in 151,624 control chromosomes in the GnomAD database, including 891 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 0.099 ( 891 hom., cov: 32)

Consequence

RALY
NM_016732.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.274
Variant links:
Genes affected
RALY (HGNC:15921): (RALY heterogeneous nuclear ribonucleoprotein) This gene encodes a member of the heterogeneous nuclear ribonucleoprotein (hnRNP) gene family. This protein may play a role in pre-mRNA splicing and in embryonic development. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2011]

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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=-0.82).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RALYNM_016732.3 linkuse as main transcriptc.-9-2282G>A intron_variant ENST00000246194.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RALYENST00000246194.8 linkuse as main transcriptc.-9-2282G>A intron_variant 1 NM_016732.3 P3Q9UKM9-1

Frequencies

GnomAD3 genomes
AF:
0.0989
AC:
14991
AN:
151504
Hom.:
889
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.172
Gnomad AMI
AF:
0.0769
Gnomad AMR
AF:
0.0602
Gnomad ASJ
AF:
0.104
Gnomad EAS
AF:
0.0950
Gnomad SAS
AF:
0.0992
Gnomad FIN
AF:
0.0849
Gnomad MID
AF:
0.0886
Gnomad NFE
AF:
0.0658
Gnomad OTH
AF:
0.0984
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0991
AC:
15023
AN:
151624
Hom.:
891
Cov.:
32
AF XY:
0.101
AC XY:
7484
AN XY:
74118
show subpopulations
Gnomad4 AFR
AF:
0.172
Gnomad4 AMR
AF:
0.0600
Gnomad4 ASJ
AF:
0.104
Gnomad4 EAS
AF:
0.0952
Gnomad4 SAS
AF:
0.0999
Gnomad4 FIN
AF:
0.0849
Gnomad4 NFE
AF:
0.0658
Gnomad4 OTH
AF:
0.0978
Alfa
AF:
0.0599
Hom.:
106
Bravo
AF:
0.0975
Asia WGS
AF:
0.0930
AC:
325
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
3.3
DANN
Benign
0.62

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.

Other links and lift over

dbSNP: rs2284390; hg19: chr20-32657590; API