chr17-75640235-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001162995.3(SMIM5):c.34G>A(p.Ala12Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000129 in 1,550,964 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/18 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001162995.3 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SMIM5 | NM_001162995.3 | c.34G>A | p.Ala12Thr | missense_variant | 2/3 | ENST00000375215.3 | NP_001156467.1 | |
RECQL5 | NM_004259.7 | c.1230-8567C>T | intron_variant | ENST00000317905.10 | NP_004250.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SMIM5 | ENST00000375215.3 | c.34G>A | p.Ala12Thr | missense_variant | 2/3 | 1 | NM_001162995.3 | ENSP00000364363.3 | ||
RECQL5 | ENST00000317905.10 | c.1230-8567C>T | intron_variant | 1 | NM_004259.7 | ENSP00000317636.5 | ||||
RECQL5 | ENST00000423245.6 | c.1149-8567C>T | intron_variant | 1 | ENSP00000394820.2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152212Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000588 AC: 9AN: 153072Hom.: 0 AF XY: 0.0000246 AC XY: 2AN XY: 81238
GnomAD4 exome AF: 0.0000114 AC: 16AN: 1398752Hom.: 0 Cov.: 31 AF XY: 0.00000725 AC XY: 5AN XY: 689898
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152212Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74372
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 02, 2024 | The c.34G>A (p.A12T) alteration is located in exon 2 (coding exon 1) of the SMIM5 gene. This alteration results from a G to A substitution at nucleotide position 34, causing the alanine (A) at amino acid position 12 to be replaced by a threonine (T). 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