NM_173848.7:c.-24+37869T>C

Variant names:

• chr8-84222293-T-C
• rs10504796
• NM_173848.7:c.-24+37869T>C

Variant summary

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

The NM_173848.7(RALYL):​c.-24+37869T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0651 in 152,238 control chromosomes in the GnomAD database, including 532 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 0.065 (532 hom., cov: 32)
• Consequence: RALYL NM_173848.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.139 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.-24+37869T>C		intron	N/A	NP_776247.3
	RALYL	NM_001413323.1		c.50+37060T>C		intron	N/A	NP_001400252.1
	RALYL	NM_001413301.1		c.38+39286T>C		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.-24+37869T>C		intron	N/A	ENSP00000430367.1	Q86SE5-1
	RALYL	ENST00000517638.5	TSL:1	c.16+37279T>C		intron	N/A	ENSP00000430128.1	Q86SE5-3
	RALYL	ENST00000521695.5	TSL:2	c.-24+38715T>C		intron	N/A	ENSP00000428667.1	Q86SE5-1

Frequencies

GnomAD3 genomes AF: 0.0650 AC: 9890 AN: 152120 Hom.: 528 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0387

Gnomad ASJ AF: 0.0213

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.0533

Gnomad FIN AF: 0.0159

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0292

Gnomad OTH AF: 0.0611

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

GnomAD4 genome AF: 0.0651 AC: 9912 AN: 152238 Hom.: 532 Cov.: 32 AF XY: 0.0642 AC XY: 4778 AN XY: 74440

African (AFR) AF: 0.142 AC: 5887 AN: 41544

American (AMR) AF: 0.0386 AC: 589 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0213 AC: 74 AN: 3470

East Asian (EAS) AF: 0.145 AC: 752 AN: 5180

South Asian (SAS) AF: 0.0534 AC: 258 AN: 4832

European-Finnish (FIN) AF: 0.0159 AC: 169 AN: 10622

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0293 AC: 1989 AN: 67998

Other (OTH) AF: 0.0657 AC: 139 AN: 2116

Alfa AF: 0.0397 Hom.: 171

Bravo AF: 0.0714

Asia WGS AF: 0.106 AC: 368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	15
DANN	Benign	0.93
PhyloP100		1.1
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: rs10504796; hg19: chr8-85134528;