GeneBe

rs5875335

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_025257.3(SLC44A4):​c.2011+65_2011+72delTTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000177 in 1,130,280 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: not found (cov: 28)
Exomes 𝑓: 0.0000018 ( 0 hom. )

Consequence

SLC44A4
NM_025257.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.323

Publications

0 publications found
Variant links:
Genes affected
SLC44A4 (HGNC:13941): (solute carrier family 44 member 4) The protein encoded by this gene may be a sodium-dependent transmembrane transport protein involved in the uptake of choline by cholinergic neurons. Defects in this gene can cause sialidosis, a lysosomal storage disease. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2010]
SLC44A4 Gene-Disease associations (from GenCC):
  • autosomal dominant nonsyndromic hearing loss
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
  • hearing loss, autosomal dominant 72
    Inheritance: AD Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)
  • nonsyndromic genetic hearing loss
    Inheritance: AD Classification: LIMITED Submitted by: ClinGen

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_025257.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
SLC44A4
NM_025257.3
MANE Select
c.2011+65_2011+72delTTTTTTTT
intron
N/ANP_079533.2A0A140VJH4
SLC44A4
NM_001178044.2
c.1885+65_1885+72delTTTTTTTT
intron
N/ANP_001171515.1Q53GD3-4
SLC44A4
NM_001178045.2
c.1783+65_1783+72delTTTTTTTT
intron
N/ANP_001171516.1A0A1U9X8K7

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
SLC44A4
ENST00000229729.11
TSL:1 MANE Select
c.2011+65_2011+72delTTTTTTTT
intron
N/AENSP00000229729.6Q53GD3-1
SLC44A4
ENST00000882851.1
c.2011+65_2011+72delTTTTTTTT
intron
N/AENSP00000552910.1
SLC44A4
ENST00000882853.1
c.2011+65_2011+72delTTTTTTTT
intron
N/AENSP00000552912.1

Frequencies

GnomAD3 genomes
Cov.:
28
GnomAD4 exome
AF:
0.00000177
AC:
2
AN:
1130280
Hom.:
0
AF XY:
0.00000349
AC XY:
2
AN XY:
572912
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
25434
American (AMR)
AF:
0.00
AC:
0
AN:
36562
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
22694
East Asian (EAS)
AF:
0.00
AC:
0
AN:
37590
South Asian (SAS)
AF:
0.0000134
AC:
1
AN:
74806
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
46862
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
4248
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
833240
Other (OTH)
AF:
0.0000205
AC:
1
AN:
48844
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.575
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<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
Cov.:
28

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.32

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs5875335; hg19: chr6-31832356; API