Variant chr1-234316592-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_173508.4(SLC35F3):c.829-10G>A variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0038 in 1,600,982 control chromosomes in the GnomAD database, including 142 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.017 ( 69 hom., cov: 33)

Exomes 𝑓: 0.0024 ( 73 hom. )

Consequence

SLC35F3
NM_173508.4 splice_polypyrimidine_tract, intron

Scores

Splicing: ADA: 0.00004350

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.607

Variant links:

Genes affected

SLC35F3 (HGNC:23616): (solute carrier family 35 member F3) Involved in thiamine transport. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

SLC35F3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 1-234316592-G-A is Benign according to our data. Variant chr1-234316592-G-A is described in ClinVar as [Benign]. Clinvar id is 782399.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0542 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC35F3	NM_173508.4 linkuse as main transcript	c.829-10G>A		splice_polypyrimidine_tract_variant, intron_variant		ENST00000366618.8	NP_775779.1
SLC35F3	NM_001300845.2 linkuse as main transcript	c.622-10G>A		splice_polypyrimidine_tract_variant, intron_variant			NP_001287774.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC35F3	ENST00000366618.8 linkuse as main transcript	c.829-10G>A		splice_polypyrimidine_tract_variant, intron_variant		2	NM_173508.4	ENSP00000355577		Q8IY50-2
SLC35F3	ENST00000366617.3 linkuse as main transcript	c.622-10G>A		splice_polypyrimidine_tract_variant, intron_variant		1		ENSP00000355576	P1	Q8IY50-1

Frequencies

GnomAD3 genomes

AF:

0.0167

AC:

2536

AN:

152162

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0561

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00694

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00104

Gnomad FIN

AF:

0.000283

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.000970

Gnomad OTH

AF:

0.0100

GnomAD3 exomes

AF:

0.00484

AC:

1212

AN:

250196

Hom.:

AF XY:

0.00391

AC XY:

529

AN XY:

135160

show subpopulations

Gnomad AFR exome

AF:

0.0579

Gnomad AMR exome

AF:

0.00314

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.000525

Gnomad FIN exome

AF:

0.000560

Gnomad NFE exome

AF:

0.00104

Gnomad OTH exome

AF:

0.00279

GnomAD4 exome

AF:

0.00244

AC:

3539

AN:

1448702

Hom.:

Cov.:

AF XY:

0.00219

AC XY:

1575

AN XY:

717794

show subpopulations

Gnomad4 AFR exome

AF:

0.0604

Gnomad4 AMR exome

AF:

0.00362

Gnomad4 ASJ exome

AF:

0.0000385

Gnomad4 EAS exome

AF:

0.0000510

Gnomad4 SAS exome

AF:

0.000478

Gnomad4 FIN exome

AF:

0.000452

Gnomad4 NFE exome

AF:

0.000897

Gnomad4 OTH exome

AF:

0.00446

GnomAD4 genome

AF:

0.0167

AC:

2539

AN:

152280

Hom.:

Cov.:

AF XY:

0.0164

AC XY:

1218

AN XY:

74456

show subpopulations

Gnomad4 AFR

AF:

0.0561

Gnomad4 AMR

AF:

0.00693

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00104

Gnomad4 FIN

AF:

0.000283

Gnomad4 NFE

AF:

0.000970

Gnomad4 OTH

AF:

0.00993

Alfa

AF:

0.0125

Hom.:

Bravo

AF:

0.0189

Asia WGS

AF:

0.00520

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Mar 29, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.37

DANN

Benign

0.65

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000043

dbscSNV1_RF

Benign

0.0

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over