chrX-72207644-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_017669.4(ERCC6L):c.1123C>T(p.Pro375Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000397 in 1,208,018 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 27 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 Uncertain significance (★).
Frequency
Consequence
NM_017669.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ERCC6L | NM_017669.4 | c.1123C>T | p.Pro375Ser | missense_variant | 2/2 | ENST00000334463.4 | NP_060139.2 | |
ERCC6L | NM_001009954.3 | c.754C>T | p.Pro252Ser | missense_variant | 3/3 | NP_001009954.1 | ||
PIN4 | NM_001170747.1 | c.312+10740G>A | intron_variant | NP_001164218.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ERCC6L | ENST00000334463.4 | c.1123C>T | p.Pro375Ser | missense_variant | 2/2 | 1 | NM_017669.4 | ENSP00000334675 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000269 AC: 3AN: 111562Hom.: 0 Cov.: 22 AF XY: 0.0000888 AC XY: 3AN XY: 33768
GnomAD3 exomes AF: 0.0000550 AC: 10AN: 181751Hom.: 0 AF XY: 0.000120 AC XY: 8AN XY: 66479
GnomAD4 exome AF: 0.0000410 AC: 45AN: 1096456Hom.: 0 Cov.: 32 AF XY: 0.0000663 AC XY: 24AN XY: 361864
GnomAD4 genome AF: 0.0000269 AC: 3AN: 111562Hom.: 0 Cov.: 22 AF XY: 0.0000888 AC XY: 3AN XY: 33768
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 21, 2023 | The c.1123C>T (p.P375S) alteration is located in exon 2 (coding exon 2) of the ERCC6L gene. This alteration results from a C to T substitution at nucleotide position 1123, causing the proline (P) at amino acid position 375 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at