15-68959037-T-G

Variant names:

• chr15-68959037-T-G
• rs12442417
• ENST00000260364.9:c.-108-15692T>G

Variant summary

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

The ENST00000260364.9(SPESP1-NOX5):​c.-108-15692T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0441 in 151,918 control chromosomes in the GnomAD database, including 347 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 0.044 (347 hom., cov: 32)
• Consequence: SPESP1-NOX5 ENST00000260364.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 2 publications found

Genes affected

SPESP1-NOX5 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000260364.9. 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
	SPESP1-NOX5	NM_001184780.2		c.29+28320T>G		intron	N/A	NP_001171709.1
	SPESP1-NOX5	NR_033671.3		n.194-15692T>G		intron	N/A
	SPESP1-NOX5	NR_033672.2		n.194-15692T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPESP1-NOX5	ENST00000260364.9	TSL:1	c.-108-15692T>G		intron	N/A	ENSP00000454143.1
	SPESP1-NOX5	ENST00000703585.1		c.29+28320T>G		intron	N/A	ENSP00000515387.1
	SPESP1-NOX5	ENST00000448182.7	TSL:1	c.-108-15692T>G		intron	N/A	ENSP00000410887.3

Frequencies

GnomAD3 genomes AF: 0.0441 AC: 6688 AN: 151800 Hom.: 348 Cov.: 32

Gnomad AFR AF: 0.0103

Gnomad AMI AF: 0.00989

Gnomad AMR AF: 0.0942

Gnomad ASJ AF: 0.0862

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.0148

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0350

Gnomad OTH AF: 0.0590

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

GnomAD4 genome AF: 0.0441 AC: 6692 AN: 151918 Hom.: 347 Cov.: 32 AF XY: 0.0461 AC XY: 3425 AN XY: 74266

African (AFR) AF: 0.0103 AC: 425 AN: 41436

American (AMR) AF: 0.0942 AC: 1436 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.0862 AC: 299 AN: 3468

East Asian (EAS) AF: 0.235 AC: 1216 AN: 5168

South Asian (SAS) AF: 0.126 AC: 609 AN: 4818

European-Finnish (FIN) AF: 0.0148 AC: 156 AN: 10554

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0350 AC: 2377 AN: 67914

Other (OTH) AF: 0.0612 AC: 129 AN: 2108

Alfa AF: 0.0404 Hom.: 277

Bravo AF: 0.0493

Asia WGS AF: 0.163 AC: 565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	5.4
DANN	Benign	0.78
PhyloP100		0.21
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs12442417; hg19: chr15-69251376;