20-34069784-G-A

Variant names:

• chr20-34069784-G-A
• rs2284390
• NM_016732.3:c.-9-2282G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016732.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RALY	NM_016732.3	MANE Select	c.-9-2282G>A		intron	N/A	NP_057951.1	Q9UKM9-1
	RALY	NM_007367.4		c.-9-2282G>A		intron	N/A	NP_031393.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RALY	ENST00000246194.8	TSL:1 MANE Select	c.-9-2282G>A		intron	N/A	ENSP00000246194.3	Q9UKM9-1
	RALY	ENST00000375114.7	TSL:1	c.-9-2282G>A		intron	N/A	ENSP00000364255.3	Q9UKM9-2
	RALY	ENST00000874581.1		c.-9-2282G>A		intron	N/A	ENSP00000544640.1

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

African (AFR) AF: 0.172 AC: 7115 AN: 41268

American (AMR) AF: 0.0600 AC: 916 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 359 AN: 3458

East Asian (EAS) AF: 0.0952 AC: 491 AN: 5158

South Asian (SAS) AF: 0.0999 AC: 479 AN: 4794

European-Finnish (FIN) AF: 0.0849 AC: 898 AN: 10580

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0658 AC: 4463 AN: 67808

Other (OTH) AF: 0.0978 AC: 205 AN: 2096

Alfa AF: 0.0662 Hom.: 141

Bravo AF: 0.0975

Asia WGS AF: 0.0930 AC: 325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.3
DANN	Benign	0.62
PhyloP100		0.27
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: rs2284390; hg19: chr20-32657590;