NM_001009608.3:c.-29-10678G>A

Variant names:

• chr20-10447498-G-A
• rs6039942
• NM_001009608.3:c.-29-10678G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001009608.3(SLX4IP):​c.-29-10678G>A 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 151,994 control chromosomes in the GnomAD database, including 759 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 (759 hom., cov: 32)
• Consequence: SLX4IP NM_001009608.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.486
• Publications: 1 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.145 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLX4IP	NM_001009608.3	MANE Select	c.-29-10678G>A		intron	N/A	NP_001009608.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLX4IP	ENST00000334534.10	TSL:1 MANE Select	c.-29-10678G>A		intron	N/A	ENSP00000335557.5
	SLX4IP	ENST00000931374.1		c.-29-10678G>A		intron	N/A	ENSP00000601433.1

Frequencies

GnomAD3 genomes AF: 0.0948 AC: 14403 AN: 151874 Hom.: 759 Cov.: 32

Gnomad AFR AF: 0.0709

Gnomad AMI AF: 0.0396

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.0455

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.0696

Gnomad FIN AF: 0.0857

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0828

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

GnomAD4 genome AF: 0.0949 AC: 14429 AN: 151994 Hom.: 759 Cov.: 32 AF XY: 0.0953 AC XY: 7082 AN XY: 74302

African (AFR) AF: 0.0709 AC: 2942 AN: 41470

American (AMR) AF: 0.128 AC: 1957 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0455 AC: 158 AN: 3470

East Asian (EAS) AF: 0.154 AC: 795 AN: 5162

South Asian (SAS) AF: 0.0702 AC: 339 AN: 4826

European-Finnish (FIN) AF: 0.0857 AC: 901 AN: 10512

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

European-Non Finnish (NFE) AF: 0.105 AC: 7110 AN: 67966

Other (OTH) AF: 0.0833 AC: 176 AN: 2112

Alfa AF: 0.0807 Hom.: 191

Bravo AF: 0.0989

Asia WGS AF: 0.106 AC: 366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.3
DANN	Benign	0.76
PhyloP100		-0.49
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: rs6039942; hg19: chr20-10428146;