NM_001012970.3:c.325+2877G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001012970.3(SPMIP3):​c.325+2877G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 152,096 control chromosomes in the GnomAD database, including 25,293 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.57 ( 25293 hom., cov: 33)

Consequence

SPMIP3
NM_001012970.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.13

Publications

5 publications found
Variant links:
Genes affected
SPMIP3 (HGNC:30435): (sperm microtubule inner protein 3)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SPMIP3NM_001012970.3 linkc.325+2877G>A intron_variant Intron 4 of 4 ENST00000308105.5 NP_001012988.1 Q5SVJ3-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SPMIP3ENST00000308105.5 linkc.325+2877G>A intron_variant Intron 4 of 4 2 NM_001012970.3 ENSP00000311218.4 Q5SVJ3-1

Frequencies

GnomAD3 genomes
AF:
0.571
AC:
86825
AN:
151978
Hom.:
25266
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.596
Gnomad AMI
AF:
0.689
Gnomad AMR
AF:
0.570
Gnomad ASJ
AF:
0.622
Gnomad EAS
AF:
0.255
Gnomad SAS
AF:
0.658
Gnomad FIN
AF:
0.555
Gnomad MID
AF:
0.465
Gnomad NFE
AF:
0.574
Gnomad OTH
AF:
0.535
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.571
AC:
86900
AN:
152096
Hom.:
25293
Cov.:
33
AF XY:
0.569
AC XY:
42284
AN XY:
74342
show subpopulations
African (AFR)
AF:
0.596
AC:
24721
AN:
41462
American (AMR)
AF:
0.570
AC:
8714
AN:
15294
Ashkenazi Jewish (ASJ)
AF:
0.622
AC:
2158
AN:
3472
East Asian (EAS)
AF:
0.255
AC:
1320
AN:
5176
South Asian (SAS)
AF:
0.659
AC:
3178
AN:
4824
European-Finnish (FIN)
AF:
0.555
AC:
5868
AN:
10564
Middle Eastern (MID)
AF:
0.463
AC:
136
AN:
294
European-Non Finnish (NFE)
AF:
0.574
AC:
39046
AN:
67984
Other (OTH)
AF:
0.535
AC:
1131
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1926
3852
5778
7704
9630
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
734
1468
2202
2936
3670
<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:
0.569
Hom.:
52228
Bravo
AF:
0.567
Asia WGS
AF:
0.459
AC:
1596
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.0030
DANN
Benign
0.41
PhyloP100
-2.1
Mutation Taster
=100/0
polymorphism (auto)

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

Other links and lift over

dbSNP: rs3123710; hg19: chr1-244544818; API