chr17-7482589-C-T
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001102614.2(SLC35G6):c.605C>T(p.Ala202Val) variant causes a missense change. The variant allele was found at a frequency of 0.000141 in 1,612,084 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000072 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00015 ( 0 hom. )
Consequence
SLC35G6
NM_001102614.2 missense
NM_001102614.2 missense
Scores
4
14
Clinical Significance
Conservation
PhyloP100: 4.98
Genes affected
SLC35G6 (HGNC:31351): (solute carrier family 35 member G6) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
ZBTB4 (HGNC:23847): (zinc finger and BTB domain containing 4) Enables several functions, including DNA-binding transcription repressor activity, RNA polymerase II-specific; methyl-CpNpG binding activity; and sequence-specific DNA binding activity. Involved in cellular response to DNA damage stimulus and negative regulation of transcription by RNA polymerase II. Located in cytosol and nuclear body. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.18214506).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC35G6 | NM_001102614.2 | c.605C>T | p.Ala202Val | missense_variant | 2/2 | ENST00000412468.4 | |
SLC35G6 | XM_047436533.1 | c.611C>T | p.Ala204Val | missense_variant | 2/2 | ||
ZBTB4 | NM_020899.4 | c.-81+1415G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC35G6 | ENST00000412468.4 | c.605C>T | p.Ala202Val | missense_variant | 2/2 | 1 | NM_001102614.2 | P1 | |
ZBTB4 | ENST00000311403.4 | c.-81+1415G>A | intron_variant | 1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152172Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000756 AC: 19AN: 251260Hom.: 0 AF XY: 0.0000957 AC XY: 13AN XY: 135786
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GnomAD4 exome AF: 0.000148 AC: 216AN: 1459912Hom.: 0 Cov.: 128 AF XY: 0.000140 AC XY: 102AN XY: 726252
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GnomAD4 genome AF: 0.0000723 AC: 11AN: 152172Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74326
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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 | Mar 28, 2023 | The c.605C>T (p.A202V) alteration is located in exon 2 (coding exon 2) of the SLC35G6 gene. This alteration results from a C to T substitution at nucleotide position 605, causing the alanine (A) at amino acid position 202 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
M_CAP
Benign
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
D;N
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Uncertain
D
Polyphen
P
Vest4
MVP
MPC
ClinPred
T
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