Genetic Variant SPMAP1:c.207+565dupT (chr17-38840617-C-CA) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_001080465.3(SPMAP1):c.207+565dupT 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 0.0038 ( 25 hom., cov: 0)

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: Likely_benign. The variant received -4 ACMG points.

BS2

High Homozygotes in GnomAd4 at 25 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPMAP1	NM_001080465.3 link	c.207+565dupT		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+565_207+566insT		intron_variant	Intron 1 of 2	2	NM_001080465.3	ENSP00000479396.1		A8MV24

Frequencies

GnomAD3 genomes

AF:

0.00382

AC:

186

AN:

48696

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00681

Gnomad AMI

AF:

0.0114

Gnomad AMR

AF:

0.00329

Gnomad ASJ

AF:

0.0111

Gnomad EAS

AF:

0.000550

Gnomad SAS

AF:

0.00225

Gnomad FIN

AF:

0.00176

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00253

Gnomad OTH

AF:

0.00172

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

GnomAD4 genome

AF:

0.00382

AC:

186

AN:

48724

Hom.:

Cov.:

AF XY:

0.00380

AC XY:

AN XY:

20540

show subpopulations

African (AFR)

AF:

0.00679

AC:

AN:

11192

American (AMR)

AF:

0.00330

AC:

AN:

2730

Ashkenazi Jewish (ASJ)

AF:

0.0111

AC:

AN:

1626

East Asian (EAS)

AF:

0.000552

AC:

AN:

1810

South Asian (SAS)

AF:

0.00225

AC:

AN:

888

European-Finnish (FIN)

AF:

0.00176

AC:

AN:

568

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00253

AC:

AN:

28828

Other (OTH)

AF:

0.00169

AC:

AN:

590

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.606

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<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

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

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17-38840617-CAAAAAAAAAAAAAAAAAAAAAAAAAA-CAAAAAAAAAAAAAAAAAAAAAAAAAAA

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