rs141063672
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2
The NM_003865.3(HESX1):c.525G>A(p.Ala175Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00172 in 1,611,574 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_003865.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HESX1 | ENST00000295934.8 | c.525G>A | p.Ala175Ala | synonymous_variant | Exon 4 of 4 | 1 | NM_003865.3 | ENSP00000295934.3 | ||
HESX1 | ENST00000647958.1 | c.525G>A | p.Ala175Ala | synonymous_variant | Exon 7 of 7 | ENSP00000498190.1 | ||||
HESX1 | ENST00000473921.2 | c.423G>A | p.Ala141Ala | synonymous_variant | Exon 3 of 3 | 5 | ENSP00000418918.1 |
Frequencies
GnomAD3 genomes AF: 0.00118 AC: 180AN: 151908Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000993 AC: 249AN: 250672Hom.: 2 AF XY: 0.00108 AC XY: 147AN XY: 135550
GnomAD4 exome AF: 0.00178 AC: 2598AN: 1459548Hom.: 2 Cov.: 30 AF XY: 0.00179 AC XY: 1300AN XY: 726088
GnomAD4 genome AF: 0.00118 AC: 180AN: 152026Hom.: 0 Cov.: 32 AF XY: 0.000982 AC XY: 73AN XY: 74318
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:2
HESX1: BP4, BP7 -
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not specified Benign:2
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Septo-optic dysplasia sequence Uncertain:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
Septo-optic dysplasia sequence;C2750027:GROWTH HORMONE DEFICIENCY WITH PITUITARY ANOMALIES Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at