chr6-44230034-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001372327.1(SLC29A1):c.442G>A(p.Val148Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000355 in 1,607,732 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001372327.1 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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC29A1 | NM_001372327.1 | c.442G>A | p.Val148Met | missense_variant | 5/13 | ENST00000371755.9 | NP_001359256.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC29A1 | ENST00000371755.9 | c.442G>A | p.Val148Met | missense_variant | 5/13 | 1 | NM_001372327.1 | ENSP00000360820 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000729 AC: 18AN: 246878Hom.: 0 AF XY: 0.0000822 AC XY: 11AN XY: 133770
GnomAD4 exome AF: 0.0000282 AC: 41AN: 1455424Hom.: 1 Cov.: 35 AF XY: 0.0000331 AC XY: 24AN XY: 724254
GnomAD4 genome AF: 0.000105 AC: 16AN: 152308Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74492
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 02, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at