chr10-99535475-A-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_145285.3(NKX2-3):c.849A>T(p.Ala283=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000953 in 1,154,296 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 0.000014 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000089 ( 0 hom. )
Consequence
NKX2-3
NM_145285.3 synonymous
NM_145285.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.00100
Genes affected
NKX2-3 (HGNC:7836): (NK2 homeobox 3) This gene encodes a homeodomain-containing transcription factor. The encoded protein is a member of the NKX family of homeodomain transcription factors. Studies of similar proteins in mouse and rat have indicated a potential role in cellular differentiation.[provided by RefSeq, Mar 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
?
Variant 10-99535475-A-T is Benign according to our data. Variant chr10-99535475-A-T is described in ClinVar as [Likely_benign]. Clinvar id is 2640748.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.001 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NKX2-3 | NM_145285.3 | c.849A>T | p.Ala283= | synonymous_variant | 2/2 | ENST00000344586.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NKX2-3 | ENST00000344586.9 | c.849A>T | p.Ala283= | synonymous_variant | 2/2 | 2 | NM_145285.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000143 AC: 2AN: 140090Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000580 AC: 1AN: 17236Hom.: 0 AF XY: 0.0000895 AC XY: 1AN XY: 11178
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GnomAD4 exome AF: 0.00000887 AC: 9AN: 1014206Hom.: 0 Cov.: 32 AF XY: 0.00000814 AC XY: 4AN XY: 491178
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GnomAD4 genome ? AF: 0.0000143 AC: 2AN: 140090Hom.: 0 Cov.: 32 AF XY: 0.0000294 AC XY: 2AN XY: 67964
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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 | Sep 01, 2022 | NKX2-3: BP4, BP7, BS2 - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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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