rs35548413

Variant summary

Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM1PM2PP3

The NM_000441.2(SLC26A4):​c.2059G>C​(p.Asp687His) variant causes a missense change. The variant allele was found at a frequency of 0.000000802 in 1,247,172 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes š‘“: 8.0e-7 ( 0 hom. )

Consequence

SLC26A4
NM_000441.2 missense

Scores

6
11
2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.39
Variant links:
Genes affected
SLC26A4 (HGNC:8818): (solute carrier family 26 member 4) Mutations in this gene are associated with Pendred syndrome, the most common form of syndromic deafness, an autosomal-recessive disease. It is highly homologous to the SLC26A3 gene; they have similar genomic structures and this gene is located 3' of the SLC26A3 gene. The encoded protein has homology to sulfate transporters. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 5 ACMG points.

PM1
In a domain STAS (size 194) in uniprot entity S26A4_HUMAN there are 17 pathogenic changes around while only 4 benign (81%) in NM_000441.2
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.766

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SLC26A4NM_000441.2 linkc.2059G>C p.Asp687His missense_variant Exon 18 of 21 ENST00000644269.2 NP_000432.1 O43511-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SLC26A4ENST00000644269.2 linkc.2059G>C p.Asp687His missense_variant Exon 18 of 21 NM_000441.2 ENSP00000494017.1 O43511-1
SLC26A4ENST00000492030.2 linkn.346G>C non_coding_transcript_exon_variant Exon 3 of 6 5
SLC26A4ENST00000644846.1 linkn.744+2298G>C intron_variant Intron 7 of 9 ENSP00000494344.1 A0A2R8Y4W7

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
8.02e-7
AC:
1
AN:
1247172
Hom.:
0
Cov.:
19
AF XY:
0.00
AC XY:
0
AN XY:
629090
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000109
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.20
BayesDel_addAF
Pathogenic
0.28
D
BayesDel_noAF
Pathogenic
0.17
CADD
Pathogenic
26
DANN
Uncertain
1.0
DEOGEN2
Uncertain
0.60
D;D
Eigen
Uncertain
0.57
Eigen_PC
Uncertain
0.55
FATHMM_MKL
Pathogenic
0.97
D
LIST_S2
Uncertain
0.87
.;D
M_CAP
Uncertain
0.24
D
MetaRNN
Pathogenic
0.77
D;D
MetaSVM
Pathogenic
0.85
D
MutationAssessor
Uncertain
2.3
M;M
PrimateAI
Uncertain
0.63
T
PROVEAN
Uncertain
-4.2
D;.
REVEL
Pathogenic
0.77
Sift
Uncertain
0.024
D;.
Sift4G
Uncertain
0.011
D;.
Polyphen
0.91
P;P
Vest4
0.71
MutPred
0.41
Gain of MoRF binding (P = 0.0594);Gain of MoRF binding (P = 0.0594);
MVP
0.98
MPC
0.067
ClinPred
1.0
D
GERP RS
4.5
Varity_R
0.49
gMVP
0.78

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr7-107344800; API