rs1232605

Positions:

• chr20-10630415-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000488816.1(SLX4IP):​c.168-5881A>G variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 151,886 control chromosomes in the GnomAD database, including 15,889 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 0.45 (15889 hom., cov: 32)
• Consequence: SLX4IP ENST00000488816.1 intron, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.941

Genes affected

SLX4IP (HGNC:16225): (SLX4 interacting protein)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLX4IP	ENST00000488816.1	c.168-5881A>G		intron_variant, NMD_transcript_variant		5		ENSP00000432784

Frequencies

GnomAD3 genomes AF: 0.454 AC: 68915 AN: 151768 Hom.: 15883 Cov.: 32

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.502

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

GnomAD4 genome AF: 0.454 AC: 68964 AN: 151886 Hom.: 15889 Cov.: 32 AF XY: 0.458 AC XY: 33997 AN XY: 74228

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.510

Gnomad4 ASJ AF: 0.439

Gnomad4 EAS AF: 0.417

Gnomad4 SAS AF: 0.538

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.418

Gnomad4 OTH AF: 0.500

Alfa AF: 0.442 Hom.: 2638

Bravo AF: 0.458

Asia WGS AF: 0.467 AC: 1623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	15
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1232605; hg19: chr20-10611063;