20-10471052-G-T

Position:

• chr20-10471052-G-T

Variant summary

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

The NM_001009608.3(SLX4IP):​c.27+12821G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 152,026 control chromosomes in the GnomAD database, including 12,357 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 0.37 (12357 hom., cov: 32)
• Consequence: SLX4IP NM_001009608.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.763

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLX4IP	NM_001009608.3	c.27+12821G>T		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+12821G>T		intron_variant		1	NM_001009608.3	ENSP00000335557	P1

Frequencies

GnomAD3 genomes AF: 0.373 AC: 56625 AN: 151908 Hom.: 12359 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.00885

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.372 AC: 56617 AN: 152026 Hom.: 12357 Cov.: 32 AF XY: 0.371 AC XY: 27565 AN XY: 74338

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.414

Gnomad4 EAS AF: 0.00887

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.552

Gnomad4 NFE AF: 0.492

Gnomad4 OTH AF: 0.364

Alfa AF: 0.431 Hom.: 1898

Bravo AF: 0.352

Asia WGS AF: 0.143 AC: 496 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.64
DANN	Benign	0.61

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: rs673034; hg19: chr20-10451700;