NM_000032.5:c.1718C>T
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4BP6_Very_StrongBS1BS2
The NM_000032.5(ALAS2):c.1718C>T(p.Ser573Phe) variant causes a missense change. The variant allele was found at a frequency of 0.000536 in 1,206,177 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 198 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000032.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ALAS2 | NM_000032.5 | c.1718C>T | p.Ser573Phe | missense_variant | Exon 11 of 11 | ENST00000650242.1 | NP_000023.2 | |
ALAS2 | NM_001037968.4 | c.1679C>T | p.Ser560Phe | missense_variant | Exon 11 of 11 | NP_001033057.1 | ||
ALAS2 | NM_001037967.4 | c.1607C>T | p.Ser536Phe | missense_variant | Exon 10 of 10 | NP_001033056.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ALAS2 | ENST00000650242.1 | c.1718C>T | p.Ser573Phe | missense_variant | Exon 11 of 11 | NM_000032.5 | ENSP00000497236.1 | |||
ALAS2 | ENST00000396198.7 | c.1679C>T | p.Ser560Phe | missense_variant | Exon 11 of 11 | 5 | ENSP00000379501.3 | |||
ALAS2 | ENST00000335854.8 | c.1607C>T | p.Ser536Phe | missense_variant | Exon 10 of 10 | 2 | ENSP00000337131.4 | |||
ALAS2 | ENST00000498636 | c.*16C>T | 3_prime_UTR_variant | Exon 5 of 5 | 3 | ENSP00000495662.1 |
Frequencies
GnomAD3 genomes AF: 0.000441 AC: 49AN: 111121Hom.: 0 Cov.: 23 AF XY: 0.000270 AC XY: 9AN XY: 33289
GnomAD3 exomes AF: 0.000272 AC: 47AN: 172744Hom.: 0 AF XY: 0.000308 AC XY: 18AN XY: 58530
GnomAD4 exome AF: 0.000545 AC: 597AN: 1095004Hom.: 0 Cov.: 31 AF XY: 0.000524 AC XY: 189AN XY: 360668
GnomAD4 genome AF: 0.000441 AC: 49AN: 111173Hom.: 0 Cov.: 23 AF XY: 0.000270 AC XY: 9AN XY: 33351
ClinVar
Submissions by phenotype
not provided Benign:5
ALAS2: BS2 -
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This variant is associated with the following publications: (PMID: 30678654) -
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ALAS2-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
X-linked sideroblastic anemia 1 Benign: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 allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at