chr21-38818503-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_005239.6(ETS2):c.668C>T(p.Pro223Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000396 in 1,614,138 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005239.6 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ETS2 | NM_005239.6 | c.668C>T | p.Pro223Leu | missense_variant | Exon 7 of 10 | ENST00000360938.8 | NP_005230.1 | |
ETS2 | NM_001256295.2 | c.1088C>T | p.Pro363Leu | missense_variant | Exon 8 of 11 | NP_001243224.1 | ||
ETS2 | XM_005260935.2 | c.668C>T | p.Pro223Leu | missense_variant | Exon 7 of 10 | XP_005260992.1 | ||
ETS2 | XM_017028290.2 | c.668C>T | p.Pro223Leu | missense_variant | Exon 7 of 10 | XP_016883779.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000440 AC: 67AN: 152132Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000509 AC: 128AN: 251452Hom.: 2 AF XY: 0.000419 AC XY: 57AN XY: 135906
GnomAD4 exome AF: 0.000391 AC: 572AN: 1461888Hom.: 2 Cov.: 32 AF XY: 0.000380 AC XY: 276AN XY: 727248
GnomAD4 genome AF: 0.000440 AC: 67AN: 152250Hom.: 0 Cov.: 32 AF XY: 0.000430 AC XY: 32AN XY: 74450
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.668C>T (p.P223L) alteration is located in exon 7 (coding exon 6) of the ETS2 gene. This alteration results from a C to T substitution at nucleotide position 668, causing the proline (P) at amino acid position 223 to be replaced by a leucine (L). 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