Genetic Variant NM_001080465.3:c.207+559_207+565delTTTTTTT (chr17-38840617-CAAAAAAA-C) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001080465.3(SPMAP1):c.207+559_207+565delTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.13 ( 293 hom., cov: 0)

Failed GnomAD Quality Control

Consequence

SPMAP1
NM_001080465.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.153

Publications

0 publications found

Variant links:

Genes affected

SPMAP1 (HGNC:34492): (sperm microtubule associated protein 1)

SPMAP1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPMAP1	NM_001080465.3 link	c.207+559_207+565delTTTTTTT		intron_variant	Intron 1 of 2	ENST00000614158.2	NP_001073934.1	A8MV24

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPMAP1	ENST00000614158.2 link	c.207+559_207+565delTTTTTTT		intron_variant	Intron 1 of 2	2	NM_001080465.3	ENSP00000479396.1		A8MV24

Frequencies

GnomAD3 genomes

AF:

0.127

AC:

6155

AN:

48534

Hom.:

293

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0441

Gnomad AMI

AF:

0.126

Gnomad AMR

AF:

0.122

Gnomad ASJ

AF:

0.0778

Gnomad EAS

AF:

0.422

Gnomad SAS

AF:

0.178

Gnomad FIN

AF:

0.325

Gnomad MID

AF:

0.125

Gnomad NFE

AF:

0.138

Gnomad OTH

AF:

0.133

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

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.127

AC:

6146

AN:

48560

Hom.:

293

Cov.:

AF XY:

0.130

AC XY:

2655

AN XY:

20476

show subpopulations

African (AFR)

AF:

0.0441

AC:

493

AN:

11174

American (AMR)

AF:

0.121

AC:

329

AN:

2724

Ashkenazi Jewish (ASJ)

AF:

0.0778

AC:

126

AN:

1620

East Asian (EAS)

AF:

0.422

AC:

767

AN:

1818

South Asian (SAS)

AF:

0.177

AC:

157

AN:

886

European-Finnish (FIN)

AF:

0.325

AC:

185

AN:

570

Middle Eastern (MID)

AF:

0.111

AC:

AN:

European-Non Finnish (NFE)

AF:

0.138

AC:

3949

AN:

28682

Other (OTH)

AF:

0.133

AC:

AN:

594

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

186

372

558

744

930

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

140

210

280

350

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.15

Mutation Taster

=100/0

polymorphism

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over