rs1427065

Positions:

• chr8-84890253-A-C
• chr8-84890253-A-G
• chr8-84890253-A-T

Variant summary

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

The NM_173848.7(RALYL):​c.858+2477A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.922 in 152,138 control chromosomes in the GnomAD database, including 64,859 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 0.92 (64859 hom., cov: 30)
• Consequence: RALYL NM_173848.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RALYL	NM_173848.7	c.858+2477A>C		intron_variant		ENST00000521268.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RALYL	ENST00000521268.6	c.858+2477A>C		intron_variant		1	NM_173848.7	P1

Frequencies

GnomAD3 genomes AF: 0.922 AC: 140227 AN: 152020 Hom.: 64807 Cov.: 30

Gnomad AFR AF: 0.981

Gnomad AMI AF: 0.941

Gnomad AMR AF: 0.941

Gnomad ASJ AF: 0.875

Gnomad EAS AF: 0.959

Gnomad SAS AF: 0.839

Gnomad FIN AF: 0.914

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.890

Gnomad OTH AF: 0.921

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

GnomAD4 genome AF: 0.922 AC: 140336 AN: 152138 Hom.: 64859 Cov.: 30 AF XY: 0.922 AC XY: 68575 AN XY: 74384

Gnomad4 AFR AF: 0.981

Gnomad4 AMR AF: 0.941

Gnomad4 ASJ AF: 0.875

Gnomad4 EAS AF: 0.959

Gnomad4 SAS AF: 0.839

Gnomad4 FIN AF: 0.914

Gnomad4 NFE AF: 0.890

Gnomad4 OTH AF: 0.917

Alfa AF: 0.895 Hom.: 78437

Bravo AF: 0.931

Asia WGS AF: 0.909 AC: 3162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.4
DANN	Benign	0.77

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: rs1427065; hg19: chr8-85802488;