Genetic Variant NM_001080465.3:c.207+560_207+565delTTTTTT (chr17-38840617-CAAAAAA-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+560_207+565delTTTTTT 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 ( 29 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:

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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+560_207+565delTTTTTT		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+560_207+565delTTTTTT		intron_variant	Intron 1 of 2	2	NM_001080465.3	ENSP00000479396.1		A8MV24

Frequencies

GnomAD3 genomes

AF:

0.126

AC:

5950

AN:

47236

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.103

Gnomad AMI

AF:

0.168

Gnomad AMR

AF:

0.163

Gnomad ASJ

AF:

0.140

Gnomad EAS

AF:

0.100

Gnomad SAS

AF:

0.107

Gnomad FIN

AF:

0.0408

Gnomad MID

AF:

0.0357

Gnomad NFE

AF:

0.134

Gnomad OTH

AF:

0.131

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:

0.126

AC:

5956

AN:

47266

Hom.:

Cov.:

AF XY:

0.123

AC XY:

2452

AN XY:

19924

show subpopulations

African (AFR)

AF:

0.102

AC:

1124

AN:

10974

American (AMR)

AF:

0.163

AC:

430

AN:

2630

Ashkenazi Jewish (ASJ)

AF:

0.140

AC:

219

AN:

1560

East Asian (EAS)

AF:

0.100

AC:

179

AN:

1782

South Asian (SAS)

AF:

0.107

AC:

AN:

854

European-Finnish (FIN)

AF:

0.0408

AC:

AN:

564

Middle Eastern (MID)

AF:

0.0370

AC:

AN:

European-Non Finnish (NFE)

AF:

0.134

AC:

3739

AN:

27842

Other (OTH)

AF:

0.133

AC:

AN:

572

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.407

Heterozygous variant carriers

226

453

679

906

1132

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

124

186

248

310

<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