rs749130159
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_003134.6(SRP14):c.370_381delCCAACAACAGCA(p.Pro124_Ala127del) variant causes a conservative inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00337 in 1,613,534 control chromosomes in the GnomAD database, including 27 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0033 ( 2 hom., cov: 33)
Exomes 𝑓: 0.0034 ( 25 hom. )
Consequence
SRP14
NM_003134.6 conservative_inframe_deletion
NM_003134.6 conservative_inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.33
Genes affected
SRP14 (HGNC:11299): (signal recognition particle 14) Enables RNA binding activity. Involved in protein targeting to ER. Located in nucleus. Part of signal recognition particle, endoplasmic reticulum targeting. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 15-40036362-CTGCTGTTGTTGG-C is Benign according to our data. Variant chr15-40036362-CTGCTGTTGTTGG-C is described in ClinVar as [Likely_benign]. Clinvar id is 2645164.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.00338 (4941/1461342) while in subpopulation MID AF= 0.0342 (197/5766). AF 95% confidence interval is 0.0303. There are 25 homozygotes in gnomad4_exome. There are 2551 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.
BS2
High AC in GnomAd4 at 503 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SRP14 | NM_003134.6 | c.370_381delCCAACAACAGCA | p.Pro124_Ala127del | conservative_inframe_deletion | Exon 5 of 5 | ENST00000267884.11 | NP_003125.3 | |
SRP14 | NM_001309434.1 | c.226_237delCCAACAACAGCA | p.Pro76_Ala79del | conservative_inframe_deletion | Exon 6 of 6 | NP_001296363.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00331 AC: 504AN: 152074Hom.: 2 Cov.: 33
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GnomAD3 exomes AF: 0.00368 AC: 925AN: 251264Hom.: 5 AF XY: 0.00386 AC XY: 524AN XY: 135842
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GnomAD4 exome AF: 0.00338 AC: 4941AN: 1461342Hom.: 25 AF XY: 0.00351 AC XY: 2551AN XY: 726968
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GnomAD4 genome AF: 0.00331 AC: 503AN: 152192Hom.: 2 Cov.: 33 AF XY: 0.00351 AC XY: 261AN XY: 74410
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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
Mar 01, 2023
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
SRP14: BS2 -
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at