rs10494096
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001144937.3(FNDC7):c.1112-28G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 1,610,268 control chromosomes in the GnomAD database, including 172,673 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.40 ( 13176 hom., cov: 30)
Exomes 𝑓: 0.46 ( 159497 hom. )
Consequence
FNDC7
NM_001144937.3 intron
NM_001144937.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0650
Genes affected
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FNDC7 | NM_001144937.3 | c.1112-28G>A | intron_variant | ENST00000370017.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FNDC7 | ENST00000370017.9 | c.1112-28G>A | intron_variant | 5 | NM_001144937.3 | P1 | |||
FNDC7 | ENST00000445274.1 | c.438-28G>A | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.402 AC: 61020AN: 151724Hom.: 13169 Cov.: 30
GnomAD3 genomes
?
AF:
AC:
61020
AN:
151724
Hom.:
Cov.:
30
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.428 AC: 106271AN: 248426Hom.: 24021 AF XY: 0.437 AC XY: 58543AN XY: 134118
GnomAD3 exomes
AF:
AC:
106271
AN:
248426
Hom.:
AF XY:
AC XY:
58543
AN XY:
134118
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.463 AC: 675394AN: 1458428Hom.: 159497 Cov.: 44 AF XY: 0.464 AC XY: 336676AN XY: 725348
GnomAD4 exome
AF:
AC:
675394
AN:
1458428
Hom.:
Cov.:
44
AF XY:
AC XY:
336676
AN XY:
725348
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.402 AC: 61041AN: 151840Hom.: 13176 Cov.: 30 AF XY: 0.402 AC XY: 29821AN XY: 74188
GnomAD4 genome
?
AF:
AC:
61041
AN:
151840
Hom.:
Cov.:
30
AF XY:
AC XY:
29821
AN XY:
74188
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1073
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at