rs2284390

chr20-34069784-G-Achr20-34069784-G-T

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.274

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]

ACMG classification

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
RALY	NM_016732.3	c.-9-2282G>A		intron_variant		ENST00000246194.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RALY	ENST00000246194.8	c.-9-2282G>A		intron_variant		1	NM_016732.3	P3

Frequencies

GnomAD3 genomes AF: 0.0989 AC: 14991 AN: 151504 Hom.: 889 Cov.: 32

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

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

Other links and lift over

dbSNP: rs2284390; hg19: chr20-32657590;