1-34761362-C-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_153212.3(GJB4):c.108C>T(p.Tyr36=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00555 in 1,614,030 control chromosomes in the GnomAD database, including 28 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0042 ( 2 hom., cov: 33)
Exomes 𝑓: 0.0057 ( 26 hom. )
Consequence
GJB4
NM_153212.3 synonymous
NM_153212.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.866
Genes affected
GJB4 (HGNC:4286): (gap junction protein beta 4) This gene encodes a transmembrane connexin protein that is a component of gap junctions. Mutations in this gene have been associated with erythrokeratodermia variabilis, progressive symmetric erythrokeratoderma and hearing impairment. [provided by RefSeq, Dec 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.68).
BP6
?
Variant 1-34761362-C-T is Benign according to our data. Variant chr1-34761362-C-T is described in ClinVar as [Benign]. Clinvar id is 710496.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.866 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.00419 (638/152312) while in subpopulation AMR AF= 0.00699 (107/15300). AF 95% confidence interval is 0.00592. There are 2 homozygotes in gnomad4. There are 286 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd at 638 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GJB4 | NM_153212.3 | c.108C>T | p.Tyr36= | synonymous_variant | 2/2 | ENST00000339480.3 | |
GJB4 | XM_011540679.3 | c.108C>T | p.Tyr36= | synonymous_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GJB4 | ENST00000339480.3 | c.108C>T | p.Tyr36= | synonymous_variant | 2/2 | 2 | NM_153212.3 | P1 | |
SMIM12 | ENST00000426886.1 | c.208-42953G>A | intron_variant, NMD_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00419 AC: 638AN: 152194Hom.: 2 Cov.: 33
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GnomAD3 exomes AF: 0.00431 AC: 1083AN: 251382Hom.: 0 AF XY: 0.00453 AC XY: 615AN XY: 135866
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GnomAD4 exome AF: 0.00570 AC: 8327AN: 1461718Hom.: 26 Cov.: 31 AF XY: 0.00557 AC XY: 4051AN XY: 727170
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 17, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at