chr2-70301851-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP6
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 (no stars).
Frequency
Consequence
NM_001329752.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
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
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