chr6-118314168-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
NM_001029858.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.473
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
?
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
?
Synonymous conserved (PhyloP=-0.473 with no splicing effect.
BS2
?
High Homozygotes in GnomAd at 7 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC35F1 | NM_001029858.4 | c.1143G>A | p.Pro381= | synonymous_variant | 8/8 | ENST00000360388.9 | |
SLC35F1 | NM_001415931.1 | c.1143G>A | p.Pro381= | synonymous_variant | 8/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC35F1 | ENST00000360388.9 | c.1143G>A | p.Pro381= | synonymous_variant | 8/8 | 1 | NM_001029858.4 | A2 | |
SLC35F1 | ENST00000621341.1 | c.966G>A | p.Pro322= | synonymous_variant | 7/7 | 5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00916 AC: 1393AN: 152052Hom.: 7 Cov.: 32
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GnomAD3 exomes AF: 0.0106 AC: 2677AN: 251482Hom.: 30 AF XY: 0.0116 AC XY: 1580AN XY: 135914
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GnomAD4 exome AF: 0.0114 AC: 16712AN: 1461878Hom.: 136 Cov.: 31 AF XY: 0.0117 AC XY: 8481AN XY: 727242
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GnomAD4 genome ? AF: 0.00915 AC: 1392AN: 152170Hom.: 7 Cov.: 32 AF XY: 0.0102 AC XY: 757AN XY: 74402
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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 submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2022 | SLC35F1: BP4, BP7, BS1, BS2 - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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