17-7482013-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate

The NM_001102614.2(SLC35G6):​c.29C>T​(p.Pro10Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000023 in 1,605,496 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 Likely benign (★).

Frequency

Genomes: 𝑓 0.000026 ( 1 hom., cov: 32)
Exomes 𝑓: 0.000023 ( 0 hom. )

Consequence

SLC35G6
NM_001102614.2 missense

Scores

18

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.87
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.03134191).
BP6
Variant 17-7482013-C-T is Benign according to our data. Variant chr17-7482013-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3444203.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SLC35G6NM_001102614.2 linkc.29C>T p.Pro10Leu missense_variant Exon 2 of 2 ENST00000412468.4 NP_001096084.1 P0C7Q6
SLC35G6XM_047436533.1 linkc.35C>T p.Pro12Leu missense_variant Exon 2 of 2 XP_047292489.1
ZBTB4NM_020899.4 linkc.-81+1991G>A intron_variant Intron 1 of 3 NP_065950.2 Q9P1Z0B3KVD4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SLC35G6ENST00000412468.4 linkc.29C>T p.Pro10Leu missense_variant Exon 2 of 2 1 NM_001102614.2 ENSP00000396523.2 P0C7Q6
ZBTB4ENST00000311403.4 linkc.-81+1991G>A intron_variant Intron 1 of 3 1 ENSP00000307858.4 Q9P1Z0

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.0000162
AC:
4
AN:
246208
Hom.:
0
AF XY:
0.0000301
AC XY:
4
AN XY:
133056
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000546
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000270
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000227
AC:
33
AN:
1453202
Hom.:
0
Cov.:
32
AF XY:
0.0000263
AC XY:
19
AN XY:
722018
show subpopulations
Gnomad4 AFR exome
AF:
0.0000603
Gnomad4 AMR exome
AF:
0.0000227
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000253
Gnomad4 SAS exome
AF:
0.0000117
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000226
Gnomad4 OTH exome
AF:
0.0000500
GnomAD4 genome
AF:
0.0000263
AC:
4
AN:
152294
Hom.:
1
Cov.:
32
AF XY:
0.0000403
AC XY:
3
AN XY:
74472
show subpopulations
Gnomad4 AFR
AF:
0.0000963
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.00000756
ExAC
AF:
0.0000330
AC:
4

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Benign:1
Nov 27, 2024
Ambry Genetics
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.052
BayesDel_addAF
Benign
-0.41
T
BayesDel_noAF
Benign
-0.66
CADD
Benign
11
DANN
Benign
0.68
DEOGEN2
Benign
0.0024
T
Eigen
Benign
-0.91
Eigen_PC
Benign
-0.73
FATHMM_MKL
Benign
0.0039
N
M_CAP
Benign
0.013
T
MetaRNN
Benign
0.031
T
MetaSVM
Benign
-0.98
T
MutationAssessor
Benign
-0.90
N
PrimateAI
Benign
0.47
T
PROVEAN
Benign
0.57
N
REVEL
Benign
0.078
Sift
Benign
1.0
T
Sift4G
Benign
0.30
T
Polyphen
0.0
B
Vest4
0.087
MutPred
0.11
Loss of glycosylation at P10 (P = 0.0458);
MVP
0.067
MPC
0.31
ClinPred
0.032
T
GERP RS
3.1
Varity_R
0.031
gMVP
0.10

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs530873703; hg19: chr17-7385332; COSMIC: COSV59497456; COSMIC: COSV59497456; API