rs12442417

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr15-68959037-T-C
• chr15-68959037-T-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.-108-15692T>C 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: 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: 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=-0.75).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPESP1-NOX5	NM_001184780.2	c.29+28320T>C		intron_variant	Intron 1 of 15		NP_001171709.1
SPESP1-NOX5	NR_033671.3	n.194-15692T>C		intron_variant	Intron 1 of 16
SPESP1-NOX5	NR_033672.2	n.194-15692T>C		intron_variant	Intron 1 of 16

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPESP1-NOX5	ENST00000260364.9	c.-108-15692T>C		intron_variant	Intron 1 of 16	1		ENSP00000454143.1
SPESP1-NOX5	ENST00000703585.1	c.29+28320T>C		intron_variant	Intron 1 of 15			ENSP00000515387.1
SPESP1-NOX5	ENST00000448182.7	c.-108-15692T>C		intron_variant	Intron 1 of 16	1		ENSP00000410887.3
SPESP1-NOX5	ENST00000557966.1	n.215-15692T>C		intron_variant	Intron 1 of 3	2

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 277

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	5.5
DANN	Benign	0.77
PhyloP100		0.21

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;