chr7-1744899-C-T
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001128636.4(ELFN1):c.303C>T(p.Asp101Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00015 in 1,557,566 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 0.00070 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000091 ( 0 hom. )
Consequence
ELFN1
NM_001128636.4 synonymous
NM_001128636.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.70
Genes affected
ELFN1 (HGNC:33154): (extracellular leucine rich repeat and fibronectin type III domain containing 1) Predicted to enable protein phosphatase inhibitor activity. Predicted to be involved in synapse organization. Predicted to be located in dendrite and excitatory synapse. Predicted to be active in extracellular matrix and extracellular space. [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=-0.56).
BP6
Variant 7-1744899-C-T is Benign according to our data. Variant chr7-1744899-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 724977.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.7 with no splicing effect.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ELFN1 | ENST00000424383.5 | c.303C>T | p.Asp101Asp | synonymous_variant | Exon 4 of 4 | 5 | NM_001128636.4 | ENSP00000456548.1 | ||
ELFN1 | ENST00000561626.4 | c.303C>T | p.Asp101Asp | synonymous_variant | Exon 3 of 3 | 2 | ENSP00000457193.1 | |||
ELFN1 | ENST00000691883.1 | c.303C>T | p.Asp101Asp | synonymous_variant | Exon 3 of 3 | ENSP00000510296.1 |
Frequencies
GnomAD3 genomes AF: 0.000697 AC: 106AN: 152182Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000182 AC: 30AN: 164538Hom.: 0 AF XY: 0.000207 AC XY: 18AN XY: 86968
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GnomAD4 exome AF: 0.0000911 AC: 128AN: 1405266Hom.: 0 Cov.: 31 AF XY: 0.0000836 AC XY: 58AN XY: 693668
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GnomAD4 genome AF: 0.000696 AC: 106AN: 152300Hom.: 0 Cov.: 33 AF XY: 0.000752 AC XY: 56AN XY: 74456
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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
May 21, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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