NM_025074.7:c.1947T>A
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_025074.7(FRAS1):c.1947T>A(p.His649Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,612,994 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. H649H) has been classified as Benign.
Frequency
Consequence
NM_025074.7 missense
Scores
Clinical Significance
Conservation
Publications
- Fraser syndromeInheritance: AR Classification: DEFINITIVE, SUPPORTIVE Submitted by: Orphanet, ClinGen
- Fraser syndrome 1Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
- renal agenesis, unilateralInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152078Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.00000807 AC: 2AN: 247960 AF XY: 0.00000743 show subpopulations
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460798Hom.: 0 Cov.: 43 AF XY: 0.00000138 AC XY: 1AN XY: 726674 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152196Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74400 show subpopulations
Age Distribution
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at