chr10-17594310-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_014241.4(HACD1):c.679C>T(p.His227Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.26 in 1,599,898 control chromosomes in the GnomAD database, including 57,144 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_014241.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HACD1 | NM_014241.4 | c.679C>T | p.His227Tyr | missense_variant | 6/7 | ENST00000361271.8 | |
HACD1 | XM_005252641.5 | c.571C>T | p.His191Tyr | missense_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HACD1 | ENST00000361271.8 | c.679C>T | p.His227Tyr | missense_variant | 6/7 | 1 | NM_014241.4 | P1 | |
HACD1 | ENST00000471481.1 | n.465C>T | non_coding_transcript_exon_variant | 3/3 | 3 | ||||
HACD1 | ENST00000498812.5 | c.*68C>T | 3_prime_UTR_variant, NMD_transcript_variant | 3/4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.252 AC: 38212AN: 151808Hom.: 5084 Cov.: 32
GnomAD3 exomes AF: 0.223 AC: 55039AN: 246782Hom.: 7080 AF XY: 0.226 AC XY: 30175AN XY: 133604
GnomAD4 exome AF: 0.261 AC: 377349AN: 1447974Hom.: 52053 Cov.: 32 AF XY: 0.259 AC XY: 186490AN XY: 719956
GnomAD4 genome AF: 0.252 AC: 38230AN: 151924Hom.: 5091 Cov.: 32 AF XY: 0.245 AC XY: 18182AN XY: 74238
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 30, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at