chr3-196226952-TCTC-T
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_152672.6(SLC51A):c.134-6_134-4delCTC variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000436 in 1,605,456 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 0.000033 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
SLC51A
NM_152672.6 splice_region, intron
NM_152672.6 splice_region, intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.26
Publications
0 publications found
Genes affected
SLC51A (HGNC:29955): (solute carrier family 51 member A) Predicted to enable protein heterodimerization activity; protein homodimerization activity; and transmembrane transporter activity. Involved in bile acid secretion. Located in basolateral plasma membrane. Implicated in progressive familial intrahepatic cholestasis. [provided by Alliance of Genome Resources, Apr 2022]
PCYT1A (HGNC:8754): (phosphate cytidylyltransferase 1A, choline) This gene belongs to the cytidylyltransferase family and is involved in the regulation of phosphatidylcholine biosynthesis. Mutations in this gene are associated with spondylometaphyseal dysplasia with cone-rod dystrophy. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Aug 2015]
PCYT1A Gene-Disease associations (from GenCC):
- spondylometaphyseal dysplasia-cone-rod dystrophy syndromeInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: ClinGen, Orphanet, Labcorp Genetics (formerly Invitae), G2P
- Leber congenital amaurosisInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
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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_152672.6. 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 |
|---|---|---|---|---|---|---|---|---|---|
| SLC51A | NM_152672.6 | MANE Select | c.134-6_134-4delCTC | splice_region intron | N/A | NP_689885.4 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| SLC51A | ENST00000296327.10 | TSL:1 MANE Select | c.134-12_134-10delCTC | intron | N/A | ENSP00000296327.5 | Q86UW1 | ||
| SLC51A | ENST00000900647.1 | c.134-12_134-10delCTC | intron | N/A | ENSP00000570706.1 | ||||
| SLC51A | ENST00000900649.1 | c.134-12_134-10delCTC | intron | N/A | ENSP00000570708.1 |
Frequencies
GnomAD3 genomes 0.0000329 AC: 5AN: 152078Hom.: 0 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
5
AN:
152078
Hom.:
Cov.:
31
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
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Gnomad OTH
AF:
GnomAD4 exome AF: 0.00000138 AC: 2AN: 1453260Hom.: 0 AF XY: 0.00000277 AC XY: 2AN XY: 722620 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
2
AN:
1453260
Hom.:
AF XY:
AC XY:
2
AN XY:
722620
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
33170
American (AMR)
AF:
AC:
0
AN:
43286
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25318
East Asian (EAS)
AF:
AC:
0
AN:
39654
South Asian (SAS)
AF:
AC:
0
AN:
85166
European-Finnish (FIN)
AF:
AC:
0
AN:
53076
Middle Eastern (MID)
AF:
AC:
2
AN:
5654
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1107982
Other (OTH)
AF:
AC:
0
AN:
59954
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.00000000770867), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.400
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
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0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
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2
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Age
GnomAD4 genome 0.0000329 AC: 5AN: 152196Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74412 show subpopulations
GnomAD4 genome
AF:
AC:
5
AN:
152196
Hom.:
Cov.:
31
AF XY:
AC XY:
2
AN XY:
74412
show subpopulations
African (AFR)
AF:
AC:
0
AN:
41530
American (AMR)
AF:
AC:
0
AN:
15282
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3470
East Asian (EAS)
AF:
AC:
0
AN:
5168
South Asian (SAS)
AF:
AC:
0
AN:
4816
European-Finnish (FIN)
AF:
AC:
0
AN:
10612
Middle Eastern (MID)
AF:
AC:
4
AN:
292
European-Non Finnish (NFE)
AF:
AC:
0
AN:
68002
Other (OTH)
AF:
AC:
1
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.545
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
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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