rs7000150

Positions:

• chr8-84268606-C-T

Variant summary

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

The NM_173848.7(RALYL):​c.-24+84182C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 151,980 control chromosomes in the GnomAD database, including 12,063 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 0.39 (12063 hom., cov: 32)
• Consequence: RALYL NM_173848.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.912

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RALYL	NM_173848.7	c.-24+84182C>T		intron_variant		ENST00000521268.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RALYL	ENST00000521268.6	c.-24+84182C>T		intron_variant		1	NM_173848.7	P1

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59158 AN: 151862 Hom.: 12061 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.389 AC: 59172 AN: 151980 Hom.: 12063 Cov.: 32 AF XY: 0.392 AC XY: 29150 AN XY: 74272

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.458

Gnomad4 ASJ AF: 0.340

Gnomad4 EAS AF: 0.526

Gnomad4 SAS AF: 0.332

Gnomad4 FIN AF: 0.471

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.384

Alfa AF: 0.406 Hom.: 5922

Bravo AF: 0.387

Asia WGS AF: 0.438 AC: 1521 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.47
DANN	Benign	0.57

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: rs7000150; hg19: chr8-85180841;