rs10504806

Variant names:

• chr8-84601140-A-G
• rs10504806
• NM_173848.7:c.256+71563A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_173848.7(RALYL):​c.256+71563A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0797 in 152,172 control chromosomes in the GnomAD database, including 1,253 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 0.080 (1253 hom., cov: 32)
• Consequence: RALYL NM_173848.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.585
• Publications: 1 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RALYL	NM_173848.7	MANE Select	c.256+71563A>G		intron	N/A	NP_776247.3
	RALYL	NM_001413323.1		c.361+71563A>G		intron	N/A	NP_001400252.1
	RALYL	NM_001413301.1		c.349+71563A>G		intron	N/A	NP_001400230.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RALYL	ENST00000521268.6	TSL:1 MANE Select	c.256+71563A>G		intron	N/A	ENSP00000430367.1	Q86SE5-1
	RALYL	ENST00000517638.5	TSL:1	c.295+71563A>G		intron	N/A	ENSP00000430128.1	Q86SE5-3
	RALYL	ENST00000521695.5	TSL:2	c.256+71563A>G		intron	N/A	ENSP00000428667.1	Q86SE5-1

Frequencies

GnomAD3 genomes AF: 0.0794 AC: 12071 AN: 152054 Hom.: 1242 Cov.: 32

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0460

Gnomad ASJ AF: 0.0714

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00785

Gnomad FIN AF: 0.0225

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0140

Gnomad OTH AF: 0.0692

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

GnomAD4 genome AF: 0.0797 AC: 12127 AN: 152172 Hom.: 1253 Cov.: 32 AF XY: 0.0775 AC XY: 5767 AN XY: 74396

African (AFR) AF: 0.236 AC: 9777 AN: 41476

American (AMR) AF: 0.0458 AC: 700 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0714 AC: 248 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5168

South Asian (SAS) AF: 0.00807 AC: 39 AN: 4834

European-Finnish (FIN) AF: 0.0225 AC: 239 AN: 10616

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0140 AC: 955 AN: 68010

Other (OTH) AF: 0.0685 AC: 145 AN: 2116

Alfa AF: 0.0614 Hom.: 124

Bravo AF: 0.0884

Asia WGS AF: 0.0260 AC: 90 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.2
DANN	Benign	0.76
PhyloP100		0.58
Mutation Taster		=100/0	polymorphism (auto)

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: rs10504806; hg19: chr8-85513375;