chr7-112487017-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_182597.3(LSMEM1):c.222C>A(p.Ser74Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000044 in 1,614,100 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_182597.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LSMEM1 | ENST00000312849.4 | c.222C>A | p.Ser74Arg | missense_variant | Exon 3 of 4 | 1 | NM_182597.3 | ENSP00000323304.3 | ||
ENSG00000288640 | ENST00000676282.1 | n.*384C>A | non_coding_transcript_exon_variant | Exon 14 of 15 | ENSP00000501830.1 | |||||
ENSG00000288640 | ENST00000676282.1 | n.*384C>A | 3_prime_UTR_variant | Exon 14 of 15 | ENSP00000501830.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251440Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135894
GnomAD4 exome AF: 0.0000465 AC: 68AN: 1461828Hom.: 0 Cov.: 30 AF XY: 0.0000413 AC XY: 30AN XY: 727218
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152272Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74466
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.222C>A (p.S74R) alteration is located in exon 3 (coding exon 2) of the LSMEM1 gene. This alteration results from a C to A substitution at nucleotide position 222, causing the serine (S) at amino acid position 74 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at