chr22-42385213-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_145912.8(NFAM1):c.761C>T(p.Pro254Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000311 in 1,605,694 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_145912.8 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 |
---|---|---|---|---|---|---|---|---|
NFAM1 | NM_145912.8 | c.761C>T | p.Pro254Leu | missense_variant | 6/6 | ENST00000329021.10 | NP_666017.1 | |
NFAM1 | NM_001371362.1 | c.605C>T | p.Pro202Leu | missense_variant | 8/8 | NP_001358291.1 | ||
NFAM1 | NM_001318323.3 | c.*51C>T | 3_prime_UTR_variant | 5/5 | NP_001305252.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NFAM1 | ENST00000329021.10 | c.761C>T | p.Pro254Leu | missense_variant | 6/6 | 1 | NM_145912.8 | ENSP00000333680 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152122Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000280 AC: 7AN: 249672Hom.: 0 AF XY: 0.0000444 AC XY: 6AN XY: 135110
GnomAD4 exome AF: 0.0000296 AC: 43AN: 1453454Hom.: 2 Cov.: 28 AF XY: 0.0000359 AC XY: 26AN XY: 723786
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152240Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74442
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 23, 2021 | 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