rs6032878

Variant names:

• chr20-10436797-T-C
• rs6032878
• NM_001009608.3:c.-30+1344T>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.-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
• Publications: 0 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=-0.87).
• 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 rank	MANE	Protein	UniProt
SLX4IP	NM_001009608.3	c.-30+1344T>C		intron_variant	Intron 1 of 7	ENST00000334534.10	NP_001009608.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLX4IP	ENST00000334534.10	c.-30+1344T>C		intron_variant	Intron 1 of 7	1	NM_001009608.3	ENSP00000335557.5

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

African (AFR) AF: 0.0715 AC: 2969 AN: 41536

American (AMR) AF: 0.126 AC: 1923 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0455 AC: 158 AN: 3472

East Asian (EAS) AF: 0.153 AC: 794 AN: 5188

South Asian (SAS) AF: 0.0705 AC: 340 AN: 4822

European-Finnish (FIN) AF: 0.0866 AC: 919 AN: 10606

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7122 AN: 68012

Other (OTH) AF: 0.0829 AC: 175 AN: 2110

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
PhyloP100		-0.066
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: rs6032878; hg19: chr20-10417445;