5-160419865-C-T

Variant names:

• chr5-160419865-C-T
• rs3811999
• ENST00000521826.5:c.-17+1726G>A

Variant summary

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

The ENST00000521826.5(SLU7):​c.-17+1726G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 151,664 control chromosomes in the GnomAD database, including 8,647 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 0.32 (8647 hom., cov: 30)
• Consequence: SLU7 ENST00000521826.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.35
• Publications: 12 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLU7	ENST00000521826.5	c.-17+1726G>A		intron_variant	Intron 1 of 4	4		ENSP00000428943.1

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49091 AN: 151546 Hom.: 8646 Cov.: 30

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.324 AC: 49095 AN: 151664 Hom.: 8647 Cov.: 30 AF XY: 0.326 AC XY: 24120 AN XY: 74096

African (AFR) AF: 0.190 AC: 7836 AN: 41290

American (AMR) AF: 0.334 AC: 5099 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1155 AN: 3466

East Asian (EAS) AF: 0.164 AC: 846 AN: 5164

South Asian (SAS) AF: 0.285 AC: 1370 AN: 4802

European-Finnish (FIN) AF: 0.440 AC: 4602 AN: 10454

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.397 AC: 26951 AN: 67940

Other (OTH) AF: 0.344 AC: 723 AN: 2104

Alfa AF: 0.363 Hom.: 32282

Bravo AF: 0.309

Asia WGS AF: 0.222 AC: 769 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	9.9
DANN	Benign	0.79
PhyloP100		2.4

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3811999; hg19: chr5-159846872;