2-26764388-C-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4BP6_ModerateBP7BS2

The NM_017877.4(SLC35F6):​c.39C>T​(p.Leu13Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0026 in 1,551,110 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0025 ( 1 hom., cov: 33)
Exomes 𝑓: 0.0026 ( 6 hom. )

Consequence

SLC35F6
NM_017877.4 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.302
Variant links:
Genes affected
SLC35F6 (HGNC:26055): (solute carrier family 35 member F6) Predicted to enable transmembrane transporter activity. Involved in negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway and positive regulation of cell population proliferation. Located in several cellular components, including lysosomal membrane; mitochondrion; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
CENPA (HGNC:1851): (centromere protein A) Centromeres are the differentiated chromosomal domains that specify the mitotic behavior of chromosomes. This gene encodes a centromere protein which contains a histone H3 related histone fold domain that is required for targeting to the centromere. Centromere protein A is proposed to be a component of a modified nucleosome or nucleosome-like structure in which it replaces 1 or both copies of conventional histone H3 in the (H3-H4)2 tetrameric core of the nucleosome particle. The protein is a replication-independent histone that is a member of the histone H3 family. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Nov 2015]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.13).
BP6
Variant 2-26764388-C-T is Benign according to our data. Variant chr2-26764388-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2650751.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.302 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 6 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SLC35F6NM_017877.4 linkc.39C>T p.Leu13Leu synonymous_variant Exon 1 of 6 ENST00000344420.10 NP_060347.2 Q8N357

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SLC35F6ENST00000344420.10 linkc.39C>T p.Leu13Leu synonymous_variant Exon 1 of 6 1 NM_017877.4 ENSP00000345528.5 Q8N357

Frequencies

GnomAD3 genomes
AF:
0.00248
AC:
378
AN:
152250
Hom.:
1
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000434
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00209
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00292
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00428
Gnomad OTH
AF:
0.00287
GnomAD3 exomes
AF:
0.00203
AC:
316
AN:
156002
Hom.:
1
AF XY:
0.00203
AC XY:
167
AN XY:
82232
show subpopulations
Gnomad AFR exome
AF:
0.000115
Gnomad AMR exome
AF:
0.000485
Gnomad ASJ exome
AF:
0.000117
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00110
Gnomad FIN exome
AF:
0.00241
Gnomad NFE exome
AF:
0.00382
Gnomad OTH exome
AF:
0.00227
GnomAD4 exome
AF:
0.00261
AC:
3655
AN:
1398740
Hom.:
6
Cov.:
31
AF XY:
0.00269
AC XY:
1854
AN XY:
689908
show subpopulations
Gnomad4 AFR exome
AF:
0.000317
Gnomad4 AMR exome
AF:
0.000784
Gnomad4 ASJ exome
AF:
0.000238
Gnomad4 EAS exome
AF:
0.0000280
Gnomad4 SAS exome
AF:
0.00109
Gnomad4 FIN exome
AF:
0.00283
Gnomad4 NFE exome
AF:
0.00304
Gnomad4 OTH exome
AF:
0.00186
GnomAD4 genome
AF:
0.00248
AC:
378
AN:
152370
Hom.:
1
Cov.:
33
AF XY:
0.00240
AC XY:
179
AN XY:
74498
show subpopulations
Gnomad4 AFR
AF:
0.000433
Gnomad4 AMR
AF:
0.00209
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00292
Gnomad4 NFE
AF:
0.00428
Gnomad4 OTH
AF:
0.00284
Alfa
AF:
0.00387
Hom.:
0
Bravo
AF:
0.00255
Asia WGS
AF:
0.000577
AC:
2
AN:
3478

ClinVar

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

Submissions by phenotype

not provided Benign:1
Apr 01, 2023
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

SLC35F6: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.13
CADD
Benign
19
DANN
Benign
0.94
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.6

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: rs142072865; hg19: chr2-26987256; API