rs4365239

Variant names:

• chr15-68952341-C-T
• rs4365239
• ENST00000260364.9:c.-109+21624C>T

Variant summary

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

The ENST00000260364.9(SPESP1-NOX5):​c.-109+21624C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 152,166 control chromosomes in the GnomAD database, including 1,446 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 0.11 (1446 hom., cov: 32)
• Consequence: SPESP1-NOX5 ENST00000260364.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921
• 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPESP1-NOX5	NM_001184780.2	c.29+21624C>T		intron_variant	Intron 1 of 15		NP_001171709.1
SPESP1-NOX5	NR_033671.3	n.193+21624C>T		intron_variant	Intron 1 of 16
SPESP1-NOX5	NR_033672.2	n.193+21624C>T		intron_variant	Intron 1 of 16

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPESP1-NOX5	ENST00000260364.9	c.-109+21624C>T		intron_variant	Intron 1 of 16	1		ENSP00000454143.1
SPESP1-NOX5	ENST00000703585.1	c.29+21624C>T		intron_variant	Intron 1 of 15			ENSP00000515387.1
SPESP1-NOX5	ENST00000448182.7	c.-109+21624C>T		intron_variant	Intron 1 of 16	1		ENSP00000410887.3
SPESP1-NOX5	ENST00000557966.1	n.214+21624C>T		intron_variant	Intron 1 of 3	2

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17431 AN: 152046 Hom.: 1437 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.0634

Gnomad ASJ AF: 0.0562

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.0804

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0605

Gnomad OTH AF: 0.0928

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

GnomAD4 genome AF: 0.115 AC: 17468 AN: 152166 Hom.: 1446 Cov.: 32 AF XY: 0.116 AC XY: 8643 AN XY: 74380

African (AFR) AF: 0.224 AC: 9312 AN: 41488

American (AMR) AF: 0.0635 AC: 971 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0562 AC: 195 AN: 3470

East Asian (EAS) AF: 0.222 AC: 1152 AN: 5178

South Asian (SAS) AF: 0.117 AC: 563 AN: 4820

European-Finnish (FIN) AF: 0.0804 AC: 852 AN: 10600

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0605 AC: 4116 AN: 67998

Other (OTH) AF: 0.0947 AC: 200 AN: 2112

Alfa AF: 0.0737 Hom.: 746

Bravo AF: 0.118

Asia WGS AF: 0.184 AC: 641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.52
PhyloP100		-0.92
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: rs4365239; hg19: chr15-69244680;