rs62530172

Variant names:

• chr8-84707992-G-A
• rs62530172
• NM_173848.7:c.257-66587G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-84707992-G-A
• chr8-84707992-G-T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_173848.7(RALYL):​c.257-66587G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: RALYL NM_173848.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.27
• Publications: 0 publications found

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

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173848.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RALYL	NM_173848.7	MANE Select	c.257-66587G>A		intron	N/A	NP_776247.3
	RALYL	NM_001413323.1		c.362-66587G>A		intron	N/A	NP_001400252.1
	RALYL	NM_001413301.1		c.350-66587G>A		intron	N/A	NP_001400230.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RALYL	ENST00000521268.6	TSL:1 MANE Select	c.257-66587G>A		intron	N/A	ENSP00000430367.1
	RALYL	ENST00000517638.5	TSL:1	c.296-66587G>A		intron	N/A	ENSP00000430128.1
	RALYL	ENST00000521695.5	TSL:2	c.257-66587G>A		intron	N/A	ENSP00000428667.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	13
DANN	Benign	0.52
PhyloP100		1.3

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

Other links and lift over

dbSNP: rs62530172; hg19: chr8-85620227;