2-70301851-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_001329752.2(FAM136A):c.161C>T(p.Ala54Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000409 in 1,552,748 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/13 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001329752.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM136A | NM_001329752.2 | c.161C>T | p.Ala54Val | missense_variant | 1/3 | ENST00000430566.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM136A | ENST00000430566.6 | c.161C>T | p.Ala54Val | missense_variant | 1/3 | 3 | NM_001329752.2 | ||
ENST00000445084.1 | n.170-104G>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00234 AC: 356AN: 152266Hom.: 1 Cov.: 34
GnomAD3 exomes AF: 0.000487 AC: 74AN: 151876Hom.: 0 AF XY: 0.000323 AC XY: 26AN XY: 80528
GnomAD4 exome AF: 0.000196 AC: 275AN: 1400364Hom.: 1 Cov.: 66 AF XY: 0.000140 AC XY: 97AN XY: 690964
GnomAD4 genome AF: 0.00236 AC: 360AN: 152384Hom.: 1 Cov.: 34 AF XY: 0.00211 AC XY: 157AN XY: 74524
ClinVar
Submissions by phenotype
FAM136A-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 15, 2020 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at