15-69013422-A-G

Variant names:

• chr15-69013422-A-G
• rs2036343
• ENST00000260364.9:c.-4-13106A>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000260364.9(SPESP1-NOX5):​c.-4-13106A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: SPESP1-NOX5 ENST00000260364.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.75
• Publications: 3 publications found

Genes affected

SPESP1-NOX5 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

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.30-13106A>G		intron	N/A	NP_001171709.1
	SPESP1-NOX5	NR_033671.3		n.298-13106A>G		intron	N/A
	SPESP1-NOX5	NR_033672.2		n.298-13106A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPESP1-NOX5	ENST00000260364.9	TSL:1	c.-4-13106A>G		intron	N/A	ENSP00000454143.1
	SPESP1-NOX5	ENST00000703585.1		c.30-13106A>G		intron	N/A	ENSP00000515387.1
	SPESP1-NOX5	ENST00000448182.7	TSL:1	c.-4-13106A>G		intron	N/A	ENSP00000410887.3

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	10
DANN	Benign	0.83
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs2036343; hg19: chr15-69305761;