chr1-169701668-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_000655.5(SELL):c.973A>G(p.Met325Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000193 in 1,581,410 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000655.5 missense
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 | UniProt |
---|---|---|---|---|---|---|---|
SELL | NM_000655.5 | c.973A>G | p.Met325Val | missense_variant | 7/9 | ENST00000236147.6 | |
SELL | NR_029467.2 | n.942A>G | non_coding_transcript_exon_variant | 5/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SELL | ENST00000236147.6 | c.973A>G | p.Met325Val | missense_variant | 7/9 | 1 | NM_000655.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152130Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000353 AC: 7AN: 198332Hom.: 0 AF XY: 0.0000378 AC XY: 4AN XY: 105750
GnomAD4 exome AF: 0.000209 AC: 299AN: 1429280Hom.: 1 Cov.: 31 AF XY: 0.000201 AC XY: 142AN XY: 707708
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152130Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74312
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 14, 2023 | The c.1012A>G (p.M338V) alteration is located in exon 7 (coding exon 7) of the SELL gene. This alteration results from a A to G substitution at nucleotide position 1012, causing the methionine (M) at amino acid position 338 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