17-77196230-A-G
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_001143998.2(SEC14L1):āc.738A>Gā(p.Arg246=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00321 in 1,614,038 control chromosomes in the GnomAD database, including 154 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.017 ( 90 hom., cov: 32)
Exomes š: 0.0017 ( 64 hom. )
Consequence
SEC14L1
NM_001143998.2 synonymous
NM_001143998.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.19
Genes affected
SEC14L1 (HGNC:10698): (SEC14 like lipid binding 1) The protein encoded by this gene belongs to the SEC14 cytosolic factor family. It has similarity to yeast SEC14 and to Japanese flying squid RALBP which suggests a possible role of the gene product in an intracellular transport system. Multiple alternatively spliced transcript variants have been found for this gene; some variants represent read-through transcripts that include exons from the upstream gene C17orf86. [provided by RefSeq, Feb 2011]
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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=-0.76).
BP6
?
Variant 17-77196230-A-G is Benign according to our data. Variant chr17-77196230-A-G is described in ClinVar as [Benign]. Clinvar id is 781390.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.19 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0585 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEC14L1 | NM_001143998.2 | c.738A>G | p.Arg246= | synonymous_variant | 8/17 | ENST00000436233.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEC14L1 | ENST00000436233.9 | c.738A>G | p.Arg246= | synonymous_variant | 8/17 | 1 | NM_001143998.2 |
Frequencies
GnomAD3 genomes ? AF: 0.0174 AC: 2654AN: 152170Hom.: 88 Cov.: 32
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GnomAD3 exomes AF: 0.00445 AC: 1119AN: 251312Hom.: 35 AF XY: 0.00311 AC XY: 422AN XY: 135848
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GnomAD4 exome AF: 0.00172 AC: 2511AN: 1461750Hom.: 64 Cov.: 30 AF XY: 0.00148 AC XY: 1075AN XY: 727196
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GnomAD4 genome ? AF: 0.0175 AC: 2663AN: 152288Hom.: 90 Cov.: 32 AF XY: 0.0165 AC XY: 1230AN XY: 74462
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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 15, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at