chr9-96013177-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_020207.7(ERCC6L2):c.4627G>A(p.Ala1543Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0911 in 1,364,476 control chromosomes in the GnomAD database, including 6,279 homozygotes. In-silico tool predicts a benign outcome for this variant. 4/4 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.088 ( 668 hom., cov: 33)
Exomes 𝑓: 0.092 ( 5611 hom. )
Consequence
ERCC6L2
NM_020207.7 missense
NM_020207.7 missense
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.125
Genes affected
ERCC6L2 (HGNC:26922): (ERCC excision repair 6 like 2) This gene encodes a member of the Snf2 family of helicase-like proteins. The encoded protein may play a role in DNA repair and mitochondrial function. Mutations in this gene have been associated with bone marrow failure syndrome 2. Alternatively spliced transcript variants that encode different protein isoforms have been described. [provided by RefSeq, Apr 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
?
Variant 9-96013177-G-A is Benign according to our data. Variant chr9-96013177-G-A is described in ClinVar as [Benign]. Clinvar id is 1167166.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ERCC6L2 | NM_020207.7 | c.4627G>A | p.Ala1543Thr | missense_variant | 19/19 | ENST00000653738.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ERCC6L2 | ENST00000653738.2 | c.4627G>A | p.Ala1543Thr | missense_variant | 19/19 | NM_020207.7 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0879 AC: 13361AN: 152030Hom.: 666 Cov.: 33
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GnomAD3 exomes AF: 0.104 AC: 25457AN: 245288Hom.: 1613 AF XY: 0.0992 AC XY: 13212AN XY: 133180
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GnomAD4 exome AF: 0.0915 AC: 110964AN: 1212328Hom.: 5611 Cov.: 32 AF XY: 0.0909 AC XY: 54637AN XY: 601066
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GnomAD4 genome ? AF: 0.0879 AC: 13374AN: 152148Hom.: 668 Cov.: 33 AF XY: 0.0899 AC XY: 6689AN XY: 74364
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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 | Feb 01, 2024 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at