X-44527356-G-A
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4
The NM_173794.4(FUNDC1):c.271C>T(p.His91Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.0000196 in 1,175,758 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 9 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000018 ( 0 hom., 0 hem., cov: 23)
Exomes 𝑓: 0.000020 ( 0 hom. 9 hem. )
Consequence
FUNDC1
NM_173794.4 missense
NM_173794.4 missense
Scores
2
6
9
Clinical Significance
Conservation
PhyloP100: 4.38
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -1 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.29731125).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FUNDC1 | NM_173794.4 | c.271C>T | p.His91Tyr | missense_variant | 4/5 | ENST00000378045.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FUNDC1 | ENST00000378045.5 | c.271C>T | p.His91Tyr | missense_variant | 4/5 | 1 | NM_173794.4 | P1 | |
FUNDC1 | ENST00000483115.1 | n.446C>T | non_coding_transcript_exon_variant | 3/4 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000180 AC: 2AN: 111400Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33630
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0000120 AC: 2AN: 167240Hom.: 0 AF XY: 0.0000181 AC XY: 1AN XY: 55158
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GnomAD4 exome AF: 0.0000197 AC: 21AN: 1064358Hom.: 0 Cov.: 24 AF XY: 0.0000267 AC XY: 9AN XY: 336656
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 05, 2023 | The c.271C>T (p.H91Y) alteration is located in exon 4 (coding exon 4) of the FUNDC1 gene. This alteration results from a C to T substitution at nucleotide position 271, causing the histidine (H) at amino acid position 91 to be replaced by a tyrosine (Y). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Uncertain
Cadd
Uncertain
Dann
Uncertain
DEOGEN2
Benign
T
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T
M_CAP
Uncertain
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D
REVEL
Benign
Sift
Benign
D
Sift4G
Benign
T
Polyphen
B
Vest4
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at