3-112155055-TAAAA-TAA
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_183061.3(SLC9C1):c.3365-8_3365-7delTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000537 in 1,266,658 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000054 ( 0 hom. )
Failed GnomAD Quality Control
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: 0.415
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]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
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.3365-8_3365-7delTT | splice_region intron | N/A | NP_898884.1 | Q4G0N8-1 | ||
| SLC9C1 | NM_001320531.2 | c.3221-8_3221-7delTT | splice_region intron | N/A | NP_001307460.1 | Q4G0N8-2 | |||
| SLC9C1 | NR_135297.2 | n.2635-8_2635-7delTT | 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.3365-8_3365-7delTT | splice_region intron | N/A | ENSP00000306627.5 | Q4G0N8-1 | ||
| SLC9C1 | ENST00000487372.5 | TSL:1 | c.3221-8_3221-7delTT | splice_region intron | N/A | ENSP00000420688.1 | Q4G0N8-2 | ||
| SLC9C1 | ENST00000471295.1 | TSL:5 | n.*1694-8_*1694-7delTT | splice_region intron | N/A | ENSP00000418371.1 | F8WCJ0 |
Frequencies
GnomAD3 genomes 0.00 AC: 0AN: 145388Hom.: 0 Cov.: 0
GnomAD3 genomes
AF:
AC:
0
AN:
145388
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
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Gnomad EAS
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Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD2 exomes AF: 0.000106 AC: 17AN: 160354 AF XY: 0.000114 show subpopulations
GnomAD2 exomes
AF:
AC:
17
AN:
160354
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
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Gnomad EAS exome
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Gnomad FIN exome
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Gnomad NFE exome
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Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000537 AC: 68AN: 1266658Hom.: 0 AF XY: 0.0000474 AC XY: 30AN XY: 632370 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
68
AN:
1266658
Hom.:
AF XY:
AC XY:
30
AN XY:
632370
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
2
AN:
28482
American (AMR)
AF:
AC:
4
AN:
32430
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
22876
East Asian (EAS)
AF:
AC:
0
AN:
35384
South Asian (SAS)
AF:
AC:
0
AN:
72292
European-Finnish (FIN)
AF:
AC:
4
AN:
40540
Middle Eastern (MID)
AF:
AC:
0
AN:
4760
European-Non Finnish (NFE)
AF:
AC:
55
AN:
977292
Other (OTH)
AF:
AC:
3
AN:
52602
⚠️ 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: 0.243
Heterozygous variant carriers
0
10
20
31
41
51
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
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Age
GnomAD4 genome 0.00 AC: 0AN: 145388Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 70412
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
145388
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
70412
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:
0
AN:
8846
Middle Eastern (MID)
AF:
AC:
0
AN:
306
European-Non Finnish (NFE)
AF:
AC:
0
AN:
66314
Other (OTH)
AF:
AC:
0
AN:
1970
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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