rs17057781

Positions:

• chr5-160419067-A-G

Variant summary

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

The NM_006425.5(SLU7):​c.-61T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 152,284 control chromosomes in the GnomAD database, including 1,585 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 0.14 (1584 hom., cov: 32)
  • Exomes 𝑓: 0.17 (1 hom.)
• Consequence: SLU7 NM_006425.5 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.141

Genes affected

SLU7 (HGNC:16939): (SLU7 homolog, splicing factor) Pre-mRNA splicing occurs in two sequential transesterification steps. The protein encoded by this gene is a splicing factor that has been found to be essential during the second catalytic step in the pre-mRNA splicing process. It associates with the spliceosome and contains a zinc knuckle motif that is found in other splicing factors and is involved in protein-nucleic acid and protein-protein interactions. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLU7	NM_006425.5	c.-61T>C		5_prime_UTR_variant	1/16	ENST00000297151.9	NP_006416.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLU7	ENST00000297151.9	c.-61T>C		5_prime_UTR_variant	1/16	1	NM_006425.5	ENSP00000297151	P1

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21569 AN: 152136 Hom.: 1584 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.158

GnomAD4 exome AF: 0.167 AC: 5 AN: 30 Hom.: 1 Cov.: 0 AF XY: 0.150 AC XY: 3 AN XY: 20

Gnomad4 ASJ exome AF: 0.00

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.167

GnomAD4 genome AF: 0.142 AC: 21579 AN: 152254 Hom.: 1584 Cov.: 32 AF XY: 0.142 AC XY: 10538 AN XY: 74436

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.146

Gnomad4 OTH AF: 0.157

Alfa AF: 0.147 Hom.: 1683

Bravo AF: 0.137

Asia WGS AF: 0.207 AC: 721 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	6.0
DANN	Benign	0.42

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: rs17057781; hg19: chr5-159846074;