rs10504793

chr8-84237599-T-C

Variant summary

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

The NM_173848.7(RALYL):c.-24+53175T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0984 in 152,138 control chromosomes in the GnomAD database, including 1,402 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 0.098 (1402 hom., cov: 32)
• Consequence: RALYL NM_173848.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130

Genes affected

RALYL (HGNC:27036): (RALY RNA binding protein like) Enables identical protein binding activity. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RALYL	NM_173848.7	c.-24+53175T>C		intron_variant		ENST00000521268.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RALYL	ENST00000521268.6	c.-24+53175T>C		intron_variant		1	NM_173848.7	P1

Frequencies

GnomAD3 genomes AF: 0.0983 AC: 14948 AN: 152020 Hom.: 1398 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.0543

Gnomad ASJ AF: 0.0386

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0170

Gnomad FIN AF: 0.0926

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0359

Gnomad OTH AF: 0.0761

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

GnomAD4 genome AF: 0.0984 AC: 14969 AN: 152138 Hom.: 1402 Cov.: 32 AF XY: 0.0968 AC XY: 7202 AN XY: 74390

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.0540

Gnomad4 ASJ AF: 0.0386

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0170

Gnomad4 FIN AF: 0.0926

Gnomad4 NFE AF: 0.0359

Gnomad4 OTH AF: 0.0753

Alfa AF: 0.0525 Hom.: 203

Bravo AF: 0.101

Asia WGS AF: 0.0210 AC: 75 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	7.7
Dann	Benign	0.48

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: rs10504793; hg19: chr8-85149834;