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GeneBe

6-118314168-G-A

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001029858.4(SLC35F1):c.1143G>A(p.Pro381=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0112 in 1,614,048 control chromosomes in the GnomAD database, including 143 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0091 ( 7 hom., cov: 32)
Exomes 𝑓: 0.011 ( 136 hom. )

Consequence

SLC35F1
NM_001029858.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.473
Variant links:
Genes affected
SLC35F1 (HGNC:21483): (solute carrier family 35 member F1) Predicted to enable transmembrane transporter activity. Predicted to be involved in transmembrane transport. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 6-118314168-G-A is Benign according to our data. Variant chr6-118314168-G-A is described in ClinVar as [Benign]. Clinvar id is 2656881.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.473 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 7 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLC35F1NM_001029858.4 linkuse as main transcriptc.1143G>A p.Pro381= synonymous_variant 8/8 ENST00000360388.9
SLC35F1NM_001415931.1 linkuse as main transcriptc.1143G>A p.Pro381= synonymous_variant 8/9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC35F1ENST00000360388.9 linkuse as main transcriptc.1143G>A p.Pro381= synonymous_variant 8/81 NM_001029858.4 A2Q5T1Q4-1
SLC35F1ENST00000621341.1 linkuse as main transcriptc.966G>A p.Pro322= synonymous_variant 7/75 P2Q5T1Q4-2

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00916
AC:
1393
AN:
152052
Hom.:
7
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00215
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00799
Gnomad ASJ
AF:
0.0265
Gnomad EAS
AF:
0.000192
Gnomad SAS
AF:
0.0135
Gnomad FIN
AF:
0.0232
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.0111
Gnomad OTH
AF:
0.0100
GnomAD3 exomes
AF:
0.0106
AC:
2677
AN:
251482
Hom.:
30
AF XY:
0.0116
AC XY:
1580
AN XY:
135914
show subpopulations
Gnomad AFR exome
AF:
0.00141
Gnomad AMR exome
AF:
0.00619
Gnomad ASJ exome
AF:
0.0195
Gnomad EAS exome
AF:
0.000109
Gnomad SAS exome
AF:
0.0144
Gnomad FIN exome
AF:
0.0203
Gnomad NFE exome
AF:
0.0112
Gnomad OTH exome
AF:
0.0137
GnomAD4 exome
AF:
0.0114
AC:
16712
AN:
1461878
Hom.:
136
Cov.:
31
AF XY:
0.0117
AC XY:
8481
AN XY:
727242
show subpopulations
Gnomad4 AFR exome
AF:
0.00149
Gnomad4 AMR exome
AF:
0.00646
Gnomad4 ASJ exome
AF:
0.0226
Gnomad4 EAS exome
AF:
0.000176
Gnomad4 SAS exome
AF:
0.0152
Gnomad4 FIN exome
AF:
0.0209
Gnomad4 NFE exome
AF:
0.0113
Gnomad4 OTH exome
AF:
0.0110
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00915
AC:
1392
AN:
152170
Hom.:
7
Cov.:
32
AF XY:
0.0102
AC XY:
757
AN XY:
74402
show subpopulations
Gnomad4 AFR
AF:
0.00214
Gnomad4 AMR
AF:
0.00798
Gnomad4 ASJ
AF:
0.0265
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.0133
Gnomad4 FIN
AF:
0.0232
Gnomad4 NFE
AF:
0.0111
Gnomad4 OTH
AF:
0.00992
Alfa
AF:
0.00899
Hom.:
4
Bravo
AF:
0.00770
Asia WGS
AF:
0.00520
AC:
18
AN:
3478
EpiCase
AF:
0.0120
EpiControl
AF:
0.0111

ClinVar

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

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenNov 01, 2022SLC35F1: BP4, BP7, BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
Cadd
Benign
2.6
Dann
Benign
0.38

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: rs41291934; hg19: chr6-118635331; COSMIC: COSV64510962; API