20-34052241-C-G

Position:

• chr20-34052241-C-G

Variant summary

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

The NM_016732.3(RALY):​c.-9-19825C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.745 in 152,150 control chromosomes in the GnomAD database, including 42,746 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 0.75 (42746 hom., cov: 32)
• Consequence: RALY NM_016732.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.842 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RALY	NM_016732.3	c.-9-19825C>G		intron_variant		ENST00000246194.8	NP_057951.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RALY	ENST00000246194.8	c.-9-19825C>G		intron_variant		1	NM_016732.3	ENSP00000246194.3

Frequencies

GnomAD3 genomes AF: 0.745 AC: 113285 AN: 152032 Hom.: 42697 Cov.: 32

Gnomad AFR AF: 0.849

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.777

Gnomad EAS AF: 0.829

Gnomad SAS AF: 0.850

Gnomad FIN AF: 0.749

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.758

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

GnomAD4 genome AF: 0.745 AC: 113386 AN: 152150 Hom.: 42746 Cov.: 32 AF XY: 0.753 AC XY: 55968 AN XY: 74370

Gnomad4 AFR AF: 0.850

Gnomad4 AMR AF: 0.712

Gnomad4 ASJ AF: 0.777

Gnomad4 EAS AF: 0.829

Gnomad4 SAS AF: 0.849

Gnomad4 FIN AF: 0.749

Gnomad4 NFE AF: 0.674

Gnomad4 OTH AF: 0.760

Alfa AF: 0.602 Hom.: 1669

Bravo AF: 0.745

Asia WGS AF: 0.809 AC: 2812 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.4
DANN	Benign	0.40

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: rs4911146; hg19: chr20-32640047;