rs1862391

Variant names:

• chr5-160421460-A-C
• rs1862391
• ENST00000521826.5:c.-17+131T>G

Your query was ambiguous. Multiple possible variants found:

• chr5-160421460-A-C
• chr5-160421460-A-G

Variant summary

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

The ENST00000521826.5(SLU7):​c.-17+131T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 152,206 control chromosomes in the GnomAD database, including 4,756 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 0.24 (4756 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: SLU7 ENST00000521826.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.166
• Publications: 4 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.309 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+131T>G		intron_variant	Intron 1 of 4	4		ENSP00000428943.1

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36131 AN: 152086 Hom.: 4750 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.238 AC: 36165 AN: 152206 Hom.: 4756 Cov.: 32 AF XY: 0.238 AC XY: 17730 AN XY: 74414

African (AFR) AF: 0.146 AC: 6046 AN: 41536

American (AMR) AF: 0.317 AC: 4842 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.294 AC: 1022 AN: 3472

East Asian (EAS) AF: 0.125 AC: 648 AN: 5184

South Asian (SAS) AF: 0.307 AC: 1480 AN: 4818

European-Finnish (FIN) AF: 0.250 AC: 2651 AN: 10586

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18747 AN: 68008

Other (OTH) AF: 0.227 AC: 479 AN: 2108

Alfa AF: 0.179 Hom.: 492

Bravo AF: 0.237

Asia WGS AF: 0.203 AC: 706 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.5
DANN	Benign	0.69
PhyloP100		0.17
PromoterAI		0.023	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1862391; hg19: chr5-159848467;