chr21-14582274-C-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001395858.1(SAMSN1):c.903G>T(p.Lys301Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00245 in 1,550,850 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001395858.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SAMSN1 | NM_001395858.1 | c.903G>T | p.Lys301Asn | missense_variant | Exon 11 of 18 | NP_001382787.1 | ||
SAMSN1 | NM_001395857.1 | c.807G>T | p.Lys269Asn | missense_variant | Exon 9 of 16 | NP_001382786.1 | ||
SAMSN1 | NM_001256370.2 | c.123G>T | p.Lys41Asn | missense_variant | Exon 2 of 9 | NP_001243299.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SAMSN1 | ENST00000285670.7 | c.123G>T | p.Lys41Asn | missense_variant | Exon 2 of 9 | 1 | ENSP00000285670.2 | |||
SAMSN1 | ENST00000647101.1 | c.807G>T | p.Lys269Asn | missense_variant | Exon 9 of 16 | ENSP00000493867.1 | ||||
SAMSN1-AS1 | ENST00000449214.1 | n.73C>A | non_coding_transcript_exon_variant | Exon 1 of 5 | 3 | |||||
SAMSN1 | ENST00000644288.1 | n.298G>T | non_coding_transcript_exon_variant | Exon 2 of 9 |
Frequencies
GnomAD3 genomes AF: 0.00198 AC: 302AN: 152196Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00170 AC: 256AN: 150508Hom.: 2 AF XY: 0.00151 AC XY: 122AN XY: 80768
GnomAD4 exome AF: 0.00250 AC: 3499AN: 1398534Hom.: 8 Cov.: 40 AF XY: 0.00240 AC XY: 1655AN XY: 689786
GnomAD4 genome AF: 0.00198 AC: 302AN: 152316Hom.: 1 Cov.: 32 AF XY: 0.00176 AC XY: 131AN XY: 74482
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 28, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at