chr1-91267768-T-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001017975.6(HFM1):c.3860A>T(p.Asp1287Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000625 in 1,520,392 control chromosomes in the GnomAD database, including 1 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 Uncertain significance (★).
Frequency
Consequence
NM_001017975.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HFM1 | NM_001017975.6 | c.3860A>T | p.Asp1287Val | missense_variant | 35/39 | ENST00000370425.8 | NP_001017975.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HFM1 | ENST00000370425.8 | c.3860A>T | p.Asp1287Val | missense_variant | 35/39 | 1 | NM_001017975.6 | ENSP00000359454.3 | ||
HFM1 | ENST00000430465.1 | c.1493A>T | p.Asp498Val | missense_variant | 16/19 | 1 | ENSP00000387661.1 | |||
HFM1 | ENST00000462405.5 | n.1786A>T | non_coding_transcript_exon_variant | 18/21 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152174Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000559 AC: 12AN: 214600Hom.: 1 AF XY: 0.0000512 AC XY: 6AN XY: 117284
GnomAD4 exome AF: 0.0000636 AC: 87AN: 1368100Hom.: 1 Cov.: 23 AF XY: 0.0000731 AC XY: 50AN XY: 684120
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152292Hom.: 0 Cov.: 33 AF XY: 0.0000671 AC XY: 5AN XY: 74464
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 07, 2024 | The c.3860A>T (p.D1287V) alteration is located in exon 35 (coding exon 34) of the HFM1 gene. This alteration results from a A to T substitution at nucleotide position 3860, causing the aspartic acid (D) at amino acid position 1287 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at