chr1-108712952-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001144937.3(FNDC7):c.19A>T(p.Thr7Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000416 in 1,551,566 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_001144937.3 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 | UniProt |
---|---|---|---|---|---|---|---|
FNDC7 | NM_001144937.3 | c.19A>T | p.Thr7Ser | missense_variant | 1/13 | ENST00000370017.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FNDC7 | ENST00000370017.9 | c.19A>T | p.Thr7Ser | missense_variant | 1/13 | 5 | NM_001144937.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000243 AC: 37AN: 152196Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000221 AC: 34AN: 154040Hom.: 0 AF XY: 0.000220 AC XY: 18AN XY: 81738
GnomAD4 exome AF: 0.000434 AC: 608AN: 1399370Hom.: 1 Cov.: 32 AF XY: 0.000438 AC XY: 302AN XY: 690194
GnomAD4 genome AF: 0.000243 AC: 37AN: 152196Hom.: 0 Cov.: 33 AF XY: 0.000282 AC XY: 21AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 13, 2024 | The c.19A>T (p.T7S) alteration is located in exon 1 (coding exon 1) of the FNDC7 gene. This alteration results from a A to T substitution at nucleotide position 19, causing the threonine (T) at amino acid position 7 to be replaced by a serine (S). 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