6-118050894-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001029858.4(SLC35F1):c.174-103551G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 151,962 control chromosomes in the GnomAD database, including 4,338 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

• Frequency: Genomes: 𝑓 0.23 (4338 hom., cov: 31)
• Consequence: SLC35F1 NM_001029858.4 intron
• Clinical Significance: association no assertion criteria provided O:1
• Conservation: PhyloP100: -0.151

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC35F1	NM_001029858.4	c.174-103551G>A		intron_variant		ENST00000360388.9
SLC35F1	NM_001415931.1	c.174-103551G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC35F1	ENST00000360388.9	c.174-103551G>A		intron_variant		1	NM_001029858.4	A2

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35338 AN: 151842 Hom.: 4335 Cov.: 31

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.238

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.233 AC: 35357 AN: 151962 Hom.: 4338 Cov.: 31 AF XY: 0.235 AC XY: 17450 AN XY: 74268

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.258

Gnomad4 EAS AF: 0.358

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.288

Gnomad4 NFE AF: 0.243

Gnomad4 OTH AF: 0.243

Alfa AF: 0.236 Hom.: 7308

Bravo AF: 0.224

Asia WGS AF: 0.277 AC: 967 AN: 3478

ClinVar

Significance: association

Submissions summary: Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Vascular endothelial growth factor (VEGF) inhibitor response Other:1

association, no assertion criteria provided

case-control

Department of Ophthalmology, College of Medicine, Hanyang University

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.78
Dann	Benign	0.53

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

Other links and lift over

dbSNP: rs11153718; hg19: chr6-118372057;