chr20-10488399-T-C

Position:

• chr20-10488399-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001009608.3(SLX4IP):​c.27+30168T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 151,898 control chromosomes in the GnomAD database, including 11,838 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 0.39 (11838 hom., cov: 31)
• Consequence: SLX4IP NM_001009608.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.776

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLX4IP	NM_001009608.3	c.27+30168T>C		intron_variant		ENST00000334534.10	NP_001009608.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLX4IP	ENST00000334534.10	c.27+30168T>C		intron_variant		1	NM_001009608.3	ENSP00000335557	P1

Frequencies

GnomAD3 genomes AF: 0.391 AC: 59372 AN: 151782 Hom.: 11832 Cov.: 31

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.483

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.350

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.391 AC: 59409 AN: 151898 Hom.: 11838 Cov.: 31 AF XY: 0.384 AC XY: 28499 AN XY: 74214

Gnomad4 AFR AF: 0.350

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.269

Gnomad4 SAS AF: 0.352

Gnomad4 FIN AF: 0.326

Gnomad4 NFE AF: 0.431

Gnomad4 OTH AF: 0.399

Alfa AF: 0.412 Hom.: 1614

Bravo AF: 0.394

Asia WGS AF: 0.274 AC: 956 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.53

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs681549; hg19: chr20-10469047;