rs6032878

Positions:

• chr20-10436797-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.-30+1344T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0949 in 152,234 control chromosomes in the GnomAD database, including 755 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 0.095 (755 hom., cov: 32)
• Consequence: SLX4IP NM_001009608.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLX4IP	NM_001009608.3	c.-30+1344T>C		intron_variant		ENST00000334534.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLX4IP	ENST00000334534.10	c.-30+1344T>C		intron_variant		1	NM_001009608.3	P1

Frequencies

GnomAD3 genomes AF: 0.0948 AC: 14426 AN: 152114 Hom.: 755 Cov.: 32

Gnomad AFR AF: 0.0714

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.0455

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.0698

Gnomad FIN AF: 0.0866

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0824

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

GnomAD4 genome AF: 0.0949 AC: 14451 AN: 152234 Hom.: 755 Cov.: 32 AF XY: 0.0952 AC XY: 7086 AN XY: 74430

Gnomad4 AFR AF: 0.0715

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.0455

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.0705

Gnomad4 FIN AF: 0.0866

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.0829

Alfa AF: 0.103 Hom.: 120

Bravo AF: 0.0988

Asia WGS AF: 0.106 AC: 368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.6
DANN	Benign	0.71

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: rs6032878; hg19: chr20-10417445;