Genetic Variant NM_001080465.3:c.207+561_207+565delTTTTT (chr17-38840617-CAAAAA-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+561_207+565delTTTTT 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 0.020 ( 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: 0.153

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+561_207+565delTTTTT		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+561_207+565delTTTTT		intron_variant	Intron 1 of 2	2	NM_001080465.3	ENSP00000479396.1		A8MV24

Frequencies

GnomAD3 genomes

AF:

0.0199

AC:

967

AN:

48496

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0494

Gnomad AMI

AF:

0.0342

Gnomad AMR

AF:

0.0132

Gnomad ASJ

AF:

0.0129

Gnomad EAS

AF:

0.00881

Gnomad SAS

AF:

0.0136

Gnomad FIN

AF:

0.00702

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0105

Gnomad OTH

AF:

0.0259

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:

0.0199

AC:

968

AN:

48524

Hom.:

Cov.:

AF XY:

0.0217

AC XY:

444

AN XY:

20442

show subpopulations

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.0494

AC:

547

AN:

11076

American (AMR)

AF:

0.0133

AC:

AN:

2716

Ashkenazi Jewish (ASJ)

AF:

0.0129

AC:

AN:

1624

East Asian (EAS)

AF:

0.00885

AC:

AN:

1808

South Asian (SAS)

AF:

0.0136

AC:

AN:

880

European-Finnish (FIN)

AF:

0.00702

AC:

AN:

570

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0105

AC:

302

AN:

28770

Other (OTH)

AF:

0.0255

AC:

AN:

588

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.394

Heterozygous variant carriers

118

158

197

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

100

<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

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