2-95853778-C-T
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001393982.1(ANKRD36C):c.6102G>A(p.Ser2034Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000237 in 1,604,428 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 30)
Exomes 𝑓: 0.000025 ( 0 hom. )
Consequence
ANKRD36C
NM_001393982.1 synonymous
NM_001393982.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.444
Genes affected
ANKRD36C (HGNC:32946): (ankyrin repeat domain 36C)
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
Variant 2-95853778-C-T is Benign according to our data. Variant chr2-95853778-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2651124.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.444 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ANKRD36C | NM_001393982.1 | c.6102G>A | p.Ser2034Ser | synonymous_variant | 84/88 | ENST00000295246.7 | NP_001380911.1 | |
ANKRD36C | NM_001310154.3 | c.6177G>A | p.Ser2059Ser | synonymous_variant | 85/89 | NP_001297083.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ANKRD36C | ENST00000295246.7 | c.6102G>A | p.Ser2034Ser | synonymous_variant | 84/88 | 5 | NM_001393982.1 | ENSP00000295246.7 | ||
ANKRD36C | ENST00000612359.4 | c.156G>A | p.Ser52Ser | synonymous_variant | 2/6 | 1 | ENSP00000485004.1 | |||
ANKRD36C | ENST00000488721.5 | n.1252G>A | non_coding_transcript_exon_variant | 4/4 | 1 | |||||
ANKRD36C | ENST00000456556.5 | c.5079G>A | p.Ser1693Ser | synonymous_variant | 64/67 | 5 | ENSP00000403302.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152140Hom.: 0 Cov.: 30
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GnomAD3 exomes AF: 0.0000214 AC: 5AN: 233184Hom.: 0 AF XY: 0.0000239 AC XY: 3AN XY: 125324
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GnomAD4 exome AF: 0.0000248 AC: 36AN: 1452288Hom.: 0 Cov.: 30 AF XY: 0.0000236 AC XY: 17AN XY: 721716
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GnomAD4 genome AF: 0.0000131 AC: 2AN: 152140Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 74328
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2023 | ANKRD36C: BP4, BP7 - |
Computational scores
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BayesDel_noAF
Benign
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Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at