Genetic Variant SPMAP1:c.207+564_207+565delTT (chr17-38840617-CAA-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+564_207+565delTT 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 0.048 ( 0 hom., cov: 0)

Failed GnomAD Quality Control

Consequence

SPMAP1
NM_001080465.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00

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+564_207+565delTT		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+564_207+565delTT		intron_variant	Intron 1 of 2	2	NM_001080465.3	ENSP00000479396.1		A8MV24

Frequencies

GnomAD3 genomes

AF:

0.0478

AC:

2309

AN:

48318

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0360

Gnomad AMI

AF:

0.0457

Gnomad AMR

AF:

0.0426

Gnomad ASJ

AF:

0.0625

Gnomad EAS

AF:

0.0198

Gnomad SAS

AF:

0.0263

Gnomad FIN

AF:

0.0357

Gnomad MID

AF:

0.0536

Gnomad NFE

AF:

0.0550

Gnomad OTH

AF:

0.0314

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:

0.0478

AC:

2309

AN:

48348

Hom.:

Cov.:

AF XY:

0.0433

AC XY:

882

AN XY:

20378

show subpopulations

African (AFR)

AF:

0.0360

AC:

400

AN:

11126

American (AMR)

AF:

0.0427

AC:

116

AN:

2718

Ashkenazi Jewish (ASJ)

AF:

0.0625

AC:

100

AN:

1600

East Asian (EAS)

AF:

0.0199

AC:

AN:

1806

South Asian (SAS)

AF:

0.0263

AC:

AN:

874

European-Finnish (FIN)

AF:

0.0357

AC:

AN:

560

Middle Eastern (MID)

AF:

0.0556

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0550

AC:

1573

AN:

28590

Other (OTH)

AF:

0.0309

AC:

AN:

582

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.400

Heterozygous variant carriers

177

265

354

442

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

104

130

<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

0.0

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

17-38840617-CAAAAAAAAAAAAAAAAAAAAAAAAAA-CAAAAAAAAAAAAAAAAAAAAAAAA

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