rs782127256
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 3P and 12B. PM1PP2BP4_ModerateBP6_ModerateBS1BS2
The NM_006306.4(SMC1A):c.2977G>T(p.Ala993Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000128 in 1,167,538 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 46 hemizygotes in GnomAD. 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 Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. A993A) has been classified as Likely benign.
Frequency
Consequence
NM_006306.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMC1A | NM_006306.4 | c.2977G>T | p.Ala993Ser | missense_variant | 20/25 | ENST00000322213.9 | |
SMC1A | NM_001281463.1 | c.2911G>T | p.Ala971Ser | missense_variant | 21/26 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMC1A | ENST00000322213.9 | c.2977G>T | p.Ala993Ser | missense_variant | 20/25 | 1 | NM_006306.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000540 AC: 6AN: 111196Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33388
GnomAD3 exomes AF: 0.0000252 AC: 3AN: 119266Hom.: 0 AF XY: 0.0000247 AC XY: 1AN XY: 40466
GnomAD4 exome AF: 0.000135 AC: 143AN: 1056342Hom.: 0 Cov.: 30 AF XY: 0.000134 AC XY: 46AN XY: 344146
GnomAD4 genome ? AF: 0.0000540 AC: 6AN: 111196Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33388
ClinVar
Submissions by phenotype
Congenital muscular hypertrophy-cerebral syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 30, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at