rs1232605

Variant names:

• chr20-10630415-A-G
• rs1232605
• ENST00000488816.1:n.166-5881A>G

Variant summary

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

The ENST00000488816.1(SLX4IP):​n.166-5881A>G variant causes a intron 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
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLX4IP	ENST00000488816.1	n.166-5881A>G		intron_variant	Intron 2 of 3	5		ENSP00000432784.1

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;