rs17079741

chr6-118131194-C-T

Variant summary

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

The NM_001029858.4(SLC35F1):c.174-23251C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0829 in 151,902 control chromosomes in the GnomAD database, including 713 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.083 (713 hom., cov: 32)
• Consequence: SLC35F1 NM_001029858.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580

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]

LOC107986523 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC35F1	NM_001029858.4	c.174-23251C>T		intron_variant		ENST00000360388.9
LOC107986523	XR_007059722.1	n.3649G>A		non_coding_transcript_exon_variant	4/4
SLC35F1	NM_001415931.1	c.174-23251C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC35F1	ENST00000360388.9	c.174-23251C>T		intron_variant		1	NM_001029858.4	A2

Frequencies

GnomAD3 genomes AF: 0.0830 AC: 12604 AN: 151784 Hom.: 719 Cov.: 32

Gnomad AFR AF: 0.0181

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.0722

Gnomad ASJ AF: 0.0873

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.0761

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

GnomAD4 genome AF: 0.0829 AC: 12587 AN: 151902 Hom.: 713 Cov.: 32 AF XY: 0.0858 AC XY: 6371 AN XY: 74216

Gnomad4 AFR AF: 0.0180

Gnomad4 AMR AF: 0.0724

Gnomad4 ASJ AF: 0.0873

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.0749

Alfa AF: 0.0835 Hom.: 78

Bravo AF: 0.0756

Asia WGS AF: 0.197 AC: 685 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	2.8
Dann	Benign	0.93

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: rs17079741; hg19: chr6-118452357;