3-112155055-TAAAA-TAAAAAAAA
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.
The NM_183061.3(SLC9C1):c.3365-10_3365-7dupTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000942 in 1,411,980 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000014 ( 0 hom., cov: 0)
Exomes 𝑓: 0.00010 ( 0 hom. )
Consequence
SLC9C1
NM_183061.3 splice_region, intron
NM_183061.3 splice_region, intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.97
Publications
6 publications found
Genes affected
SLC9C1 (HGNC:31401): (solute carrier family 9 member C1) Predicted to enable potassium:proton antiporter activity and sodium:proton antiporter activity. Predicted to be involved in potassium ion transmembrane transport; regulation of intracellular pH; and sodium ion import across plasma membrane. Predicted to act upstream of or within flagellated sperm motility. Predicted to be located in motile cilium. Predicted to be integral component of membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_183061.3. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| SLC9C1 | NM_183061.3 | MANE Select | c.3365-10_3365-7dupTTTT | splice_region intron | N/A | NP_898884.1 | Q4G0N8-1 | ||
| SLC9C1 | NM_001320531.2 | c.3221-10_3221-7dupTTTT | splice_region intron | N/A | NP_001307460.1 | Q4G0N8-2 | |||
| SLC9C1 | NR_135297.2 | n.2635-10_2635-7dupTTTT | splice_region intron | N/A |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| SLC9C1 | ENST00000305815.10 | TSL:2 MANE Select | c.3365-7_3365-6insTTTT | splice_region intron | N/A | ENSP00000306627.5 | Q4G0N8-1 | ||
| SLC9C1 | ENST00000487372.5 | TSL:1 | c.3221-7_3221-6insTTTT | splice_region intron | N/A | ENSP00000420688.1 | Q4G0N8-2 | ||
| SLC9C1 | ENST00000471295.1 | TSL:5 | n.*1694-7_*1694-6insTTTT | splice_region intron | N/A | ENSP00000418371.1 | F8WCJ0 |
Frequencies
GnomAD3 genomes 0.0000138 AC: 2AN: 145384Hom.: 0 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
2
AN:
145384
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD2 exomes AF: 0.000287 AC: 46AN: 160354 AF XY: 0.000297 show subpopulations
GnomAD2 exomes
AF:
AC:
46
AN:
160354
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000103 AC: 131AN: 1266596Hom.: 0 Cov.: 30 AF XY: 0.000108 AC XY: 68AN XY: 632272 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
131
AN:
1266596
Hom.:
Cov.:
30
AF XY:
AC XY:
68
AN XY:
632272
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
4
AN:
28482
American (AMR)
AF:
AC:
13
AN:
32398
Ashkenazi Jewish (ASJ)
AF:
AC:
4
AN:
22888
East Asian (EAS)
AF:
AC:
4
AN:
35338
South Asian (SAS)
AF:
AC:
34
AN:
72148
European-Finnish (FIN)
AF:
AC:
3
AN:
40552
Middle Eastern (MID)
AF:
AC:
0
AN:
4762
European-Non Finnish (NFE)
AF:
AC:
66
AN:
977410
Other (OTH)
AF:
AC:
3
AN:
52618
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 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: 0.255
Heterozygous variant carriers
0
18
35
53
70
88
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
4
8
12
16
20
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome 0.0000138 AC: 2AN: 145384Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 70408 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome
AF:
AC:
2
AN:
145384
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
70408
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
39514
American (AMR)
AF:
AC:
0
AN:
14512
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3390
East Asian (EAS)
AF:
AC:
0
AN:
5034
South Asian (SAS)
AF:
AC:
0
AN:
4614
European-Finnish (FIN)
AF:
AC:
1
AN:
8844
Middle Eastern (MID)
AF:
AC:
0
AN:
306
European-Non Finnish (NFE)
AF:
AC:
1
AN:
66312
Other (OTH)
AF:
AC:
0
AN:
1970
⚠️ 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: 0.300
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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