X-53411825-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP2PP3
The NM_006306.4(SMC1A):c.1190A>T(p.Asn397Ile) variant causes a missense change. The variant allele was found at a frequency of 0.00000182 in 1,098,038 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N397S) has been classified as Uncertain significance.
Frequency
Consequence
NM_006306.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMC1A | NM_006306.4 | c.1190A>T | p.Asn397Ile | missense_variant | 7/25 | ENST00000322213.9 | |
SMC1A | NM_001281463.1 | c.1124A>T | p.Asn375Ile | missense_variant | 8/26 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMC1A | ENST00000322213.9 | c.1190A>T | p.Asn397Ile | missense_variant | 7/25 | 1 | NM_006306.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 22
GnomAD4 exome AF: 0.00000182 AC: 2AN: 1098038Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 1AN XY: 363394
GnomAD4 genome Cov.: 22
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at