chr14-106627284-G-C
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The ENST00000390629.3(IGHV4-59):āc.315C>Gā(p.Thr105=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000211 in 1,422,832 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 (ā ).
Frequency
Genomes: not found (cov: 39)
Exomes š: 0.0000021 ( 0 hom. )
Consequence
IGHV4-59
ENST00000390629.3 synonymous
ENST00000390629.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -6.06
Genes affected
IGHV4-59 (HGNC:5654): (immunoglobulin heavy variable 4-59) Predicted to enable antigen binding activity and immunoglobulin receptor binding activity. Predicted to be involved in several processes, including activation of immune response; defense response to other organism; and phagocytosis. Predicted to be located in extracellular region and plasma membrane. Predicted to be part of immunoglobulin complex, circulating. Predicted to be active in external side of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.88).
BP6
Variant 14-106627284-G-C is Benign according to our data. Variant chr14-106627284-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 2644933.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-6.06 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IGHV4-59 | ENST00000390629.3 | c.315C>G | p.Thr105= | synonymous_variant | 2/2 | P1 |
Frequencies
GnomAD3 genomes Cov.: 39
GnomAD3 genomes
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39
GnomAD3 exomes AF: 0.0000122 AC: 3AN: 245482Hom.: 0 AF XY: 0.0000150 AC XY: 2AN XY: 133608
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GnomAD4 exome AF: 0.00000211 AC: 3AN: 1422832Hom.: 0 Cov.: 27 AF XY: 0.00000422 AC XY: 3AN XY: 710326
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GnomAD4 genome Cov.: 39
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39
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, 2022 | IGHV4-59: BP4, BP7 - |
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