chrX-72207740-C-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_017669.4(ERCC6L):c.1027G>C(p.Ala343Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000901 in 1,209,659 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 40 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_017669.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ERCC6L | NM_017669.4 | c.1027G>C | p.Ala343Pro | missense_variant | 2/2 | ENST00000334463.4 | |
ERCC6L | NM_001009954.3 | c.658G>C | p.Ala220Pro | missense_variant | 3/3 | ||
PIN4 | NM_001170747.1 | c.312+10836C>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ERCC6L | ENST00000334463.4 | c.1027G>C | p.Ala343Pro | missense_variant | 2/2 | 1 | NM_017669.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000358 AC: 4AN: 111736Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33900
GnomAD3 exomes AF: 0.0000549 AC: 10AN: 182291Hom.: 0 AF XY: 0.0000890 AC XY: 6AN XY: 67395
GnomAD4 exome AF: 0.0000956 AC: 105AN: 1097923Hom.: 0 Cov.: 32 AF XY: 0.000110 AC XY: 40AN XY: 363301
GnomAD4 genome ? AF: 0.0000358 AC: 4AN: 111736Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33900
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2022 | ERCC6L: BP4, BS2; PIN4: BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at