7-107710094-C-T
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_000441.2(SLC26A4):c.2130C>T(p.Asp710Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00369 in 1,611,564 control chromosomes in the GnomAD database, including 175 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000441.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC26A4 | ENST00000644269.2 | c.2130C>T | p.Asp710Asp | synonymous_variant | Exon 19 of 21 | NM_000441.2 | ENSP00000494017.1 | |||
SLC26A4 | ENST00000644846.1 | n.*32C>T | non_coding_transcript_exon_variant | Exon 8 of 10 | ENSP00000494344.1 | |||||
SLC26A4 | ENST00000644846.1 | n.*32C>T | 3_prime_UTR_variant | Exon 8 of 10 | ENSP00000494344.1 | |||||
SLC26A4 | ENST00000492030.2 | n.377-61C>T | intron_variant | Intron 3 of 5 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0189 AC: 2877AN: 152152Hom.: 78 Cov.: 32
GnomAD3 exomes AF: 0.00492 AC: 1237AN: 251266Hom.: 39 AF XY: 0.00362 AC XY: 492AN XY: 135784
GnomAD4 exome AF: 0.00210 AC: 3062AN: 1459294Hom.: 97 Cov.: 29 AF XY: 0.00179 AC XY: 1302AN XY: 726174
GnomAD4 genome AF: 0.0190 AC: 2887AN: 152270Hom.: 78 Cov.: 32 AF XY: 0.0180 AC XY: 1341AN XY: 74452
ClinVar
Submissions by phenotype
not specified Benign:4
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This variant is classified as benign due to a common occurrence in control poula tions (dbSNP - rs17154347). -
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
not provided Benign:4
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Pendred syndrome Benign:2
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This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
Autosomal recessive nonsyndromic hearing loss 4 Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at