rs2036343

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr15-69013422-A-C
• chr15-69013422-A-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.-4-13106A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0654 in 152,296 control chromosomes in the GnomAD database, including 394 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 0.065 (394 hom., 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPESP1-NOX5	NM_001184780.2	c.30-13106A>C		intron_variant	Intron 1 of 15		NP_001171709.1
SPESP1-NOX5	NR_033671.3	n.298-13106A>C		intron_variant	Intron 2 of 16
SPESP1-NOX5	NR_033672.2	n.298-13106A>C		intron_variant	Intron 2 of 16

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPESP1-NOX5	ENST00000260364.9	c.-4-13106A>C		intron_variant	Intron 2 of 16	1		ENSP00000454143.1
SPESP1-NOX5	ENST00000703585.1	c.30-13106A>C		intron_variant	Intron 1 of 15			ENSP00000515387.1
SPESP1-NOX5	ENST00000448182.7	c.-4-13106A>C		intron_variant	Intron 2 of 16	1		ENSP00000410887.3
SPESP1-NOX5	ENST00000557966.1	n.319-13106A>C		intron_variant	Intron 2 of 3	2

Frequencies

GnomAD3 genomes AF: 0.0654 AC: 9955 AN: 152178 Hom.: 394 Cov.: 33

Gnomad AFR AF: 0.0857

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.0429

Gnomad ASJ AF: 0.0360

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.0929

Gnomad FIN AF: 0.0581

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0504

Gnomad OTH AF: 0.0574

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

GnomAD4 genome AF: 0.0654 AC: 9961 AN: 152296 Hom.: 394 Cov.: 33 AF XY: 0.0660 AC XY: 4917 AN XY: 74460

African (AFR) AF: 0.0856 AC: 3559 AN: 41570

American (AMR) AF: 0.0431 AC: 659 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0360 AC: 125 AN: 3468

East Asian (EAS) AF: 0.178 AC: 920 AN: 5178

South Asian (SAS) AF: 0.0928 AC: 448 AN: 4828

European-Finnish (FIN) AF: 0.0581 AC: 616 AN: 10602

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0504 AC: 3430 AN: 68032

Other (OTH) AF: 0.0573 AC: 121 AN: 2112

Alfa AF: 0.0586 Hom.: 28

Bravo AF: 0.0646

Asia WGS AF: 0.127 AC: 440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	9.9
DANN	Benign	0.80
PhyloP100		1.7
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: rs2036343; hg19: chr15-69305761;