1-169691801-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_000655.5(SELL):āc.1102A>Gā(p.Met368Val) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000305 in 1,375,202 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/20 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_000655.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SELL | NM_000655.5 | c.1102A>G | p.Met368Val | missense_variant, splice_region_variant | 9/9 | ENST00000236147.6 | NP_000646.3 | |
SELL | NR_029467.2 | n.1071A>G | splice_region_variant, non_coding_transcript_exon_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SELL | ENST00000236147.6 | c.1102A>G | p.Met368Val | missense_variant, splice_region_variant | 9/9 | 1 | NM_000655.5 | ENSP00000236147.5 | ||
SELL | ENST00000650983.1 | c.1141A>G | p.Met381Val | missense_variant, splice_region_variant | 9/9 | ENSP00000498227.1 | ||||
SELL | ENST00000497295.1 | c.94A>G | p.Met32Val | missense_variant, splice_region_variant | 3/3 | 5 | ENSP00000498707.1 | |||
C1orf112 | ENST00000498289.5 | n.851+7869T>C | intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152170Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000522 AC: 7AN: 134142Hom.: 0 AF XY: 0.0000408 AC XY: 3AN XY: 73536
GnomAD4 exome AF: 0.0000270 AC: 33AN: 1223032Hom.: 0 Cov.: 24 AF XY: 0.0000383 AC XY: 23AN XY: 599932
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152170Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 10, 2024 | The c.1141A>G (p.M381V) alteration is located in exon 9 (coding exon 9) of the SELL gene. This alteration results from a A to G substitution at nucleotide position 1141, causing the methionine (M) at amino acid position 381 to be replaced by a valine (V). 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