rs1232605

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.500 AC: 20681 AN: 41372

American (AMR) AF: 0.510 AC: 7795 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1524 AN: 3468

East Asian (EAS) AF: 0.417 AC: 2138 AN: 5132

South Asian (SAS) AF: 0.538 AC: 2595 AN: 4822

European-Finnish (FIN) AF: 0.386 AC: 4078 AN: 10560

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.418 AC: 28435 AN: 67950

Other (OTH) AF: 0.500 AC: 1054 AN: 2106

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
PhyloP100		0.94

Splicing

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

Other links and lift over

dbSNP: rs1232605; hg19: chr20-10611063;