20-10488399-T-C

Variant names:

• chr20-10488399-T-C
• rs681549
• NM_001009608.3:c.27+30168T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001009608.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLX4IP	NM_001009608.3	MANE Select	c.27+30168T>C		intron	N/A	NP_001009608.1	Q5VYV7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLX4IP	ENST00000334534.10	TSL:1 MANE Select	c.27+30168T>C		intron	N/A	ENSP00000335557.5	Q5VYV7
	SLX4IP	ENST00000931374.1		c.27+30168T>C		intron	N/A	ENSP00000601433.1

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

African (AFR) AF: 0.350 AC: 14502 AN: 41416

American (AMR) AF: 0.410 AC: 6250 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1500 AN: 3468

East Asian (EAS) AF: 0.269 AC: 1384 AN: 5146

South Asian (SAS) AF: 0.352 AC: 1687 AN: 4794

European-Finnish (FIN) AF: 0.326 AC: 3447 AN: 10584

Middle Eastern (MID) AF: 0.353 AC: 103 AN: 292

European-Non Finnish (NFE) AF: 0.431 AC: 29257 AN: 67928

Other (OTH) AF: 0.399 AC: 840 AN: 2104

Alfa AF: 0.408 Hom.: 1649

Bravo AF: 0.394

Asia WGS AF: 0.274 AC: 956 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.53
PhyloP100		-0.78
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs681549; hg19: chr20-10469047;