20-34057745-C-T

Position:

• chr20-34057745-C-T

Variant summary

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

The NM_016732.3(RALY):​c.-9-14321C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.625 in 151,140 control chromosomes in the GnomAD database, including 30,725 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 0.63 (30725 hom., cov: 29)
• Consequence: RALY NM_016732.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0860

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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RALY	NM_016732.3	c.-9-14321C>T		intron_variant		ENST00000246194.8	NP_057951.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RALY	ENST00000246194.8	c.-9-14321C>T		intron_variant		1	NM_016732.3	ENSP00000246194	P3

Frequencies

GnomAD3 genomes AF: 0.625 AC: 94437 AN: 151044 Hom.: 30716 Cov.: 29

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.773

Gnomad EAS AF: 0.829

Gnomad SAS AF: 0.851

Gnomad FIN AF: 0.751

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.669

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

GnomAD4 genome AF: 0.625 AC: 94479 AN: 151140 Hom.: 30725 Cov.: 29 AF XY: 0.638 AC XY: 47057 AN XY: 73814

Gnomad4 AFR AF: 0.434

Gnomad4 AMR AF: 0.660

Gnomad4 ASJ AF: 0.773

Gnomad4 EAS AF: 0.829

Gnomad4 SAS AF: 0.851

Gnomad4 FIN AF: 0.751

Gnomad4 NFE AF: 0.673

Gnomad4 OTH AF: 0.671

Alfa AF: 0.642 Hom.: 10103

Bravo AF: 0.606

Asia WGS AF: 0.786 AC: 2733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.3
DANN	Benign	0.53

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: rs8119937; hg19: chr20-32645551;