7-107666761-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000441.2(SLC26A4):​c.304+3326C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 151,904 control chromosomes in the GnomAD database, including 6,543 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.29 ( 6543 hom., cov: 31)

Consequence

SLC26A4
NM_000441.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.382
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 Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SLC26A4NM_000441.2 linkuse as main transcriptc.304+3326C>T intron_variant ENST00000644269.2 NP_000432.1 O43511-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SLC26A4ENST00000644269.2 linkuse as main transcriptc.304+3326C>T intron_variant NM_000441.2 ENSP00000494017.1 O43511-1
SLC26A4ENST00000440056.1 linkuse as main transcriptc.304+3326C>T intron_variant 4 ENSP00000394760.1 C9JQG1

Frequencies

GnomAD3 genomes
AF:
0.288
AC:
43777
AN:
151788
Hom.:
6542
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.262
Gnomad AMI
AF:
0.330
Gnomad AMR
AF:
0.246
Gnomad ASJ
AF:
0.333
Gnomad EAS
AF:
0.241
Gnomad SAS
AF:
0.220
Gnomad FIN
AF:
0.317
Gnomad MID
AF:
0.196
Gnomad NFE
AF:
0.316
Gnomad OTH
AF:
0.271
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.288
AC:
43807
AN:
151904
Hom.:
6543
Cov.:
31
AF XY:
0.288
AC XY:
21400
AN XY:
74204
show subpopulations
Gnomad4 AFR
AF:
0.262
Gnomad4 AMR
AF:
0.246
Gnomad4 ASJ
AF:
0.333
Gnomad4 EAS
AF:
0.241
Gnomad4 SAS
AF:
0.221
Gnomad4 FIN
AF:
0.317
Gnomad4 NFE
AF:
0.316
Gnomad4 OTH
AF:
0.270
Alfa
AF:
0.301
Hom.:
7935
Bravo
AF:
0.278
Asia WGS
AF:
0.220
AC:
767
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.45
DANN
Benign
0.19

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2701688; hg19: chr7-107307206; API