6-118131194-C-T

Variant names:

• chr6-118131194-C-T
• rs17079741
• NM_001029858.4:c.174-23251C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001029858.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC35F1	NM_001029858.4	MANE Select	c.174-23251C>T		intron	N/A	NP_001025029.2
	SLC35F1	NM_001415931.1		c.174-23251C>T		intron	N/A	NP_001402860.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC35F1	ENST00000360388.9	TSL:1 MANE Select	c.174-23251C>T		intron	N/A	ENSP00000353557.4

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

African (AFR) AF: 0.0180 AC: 745 AN: 41446

American (AMR) AF: 0.0724 AC: 1103 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.0873 AC: 303 AN: 3472

East Asian (EAS) AF: 0.176 AC: 907 AN: 5156

South Asian (SAS) AF: 0.268 AC: 1292 AN: 4818

European-Finnish (FIN) AF: 0.102 AC: 1069 AN: 10510

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6890 AN: 67942

Other (OTH) AF: 0.0749 AC: 158 AN: 2110

Alfa AF: 0.0885 Hom.: 177

Bravo AF: 0.0756

Asia WGS AF: 0.197 AC: 685 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.8
DANN	Benign	0.93
PhyloP100		-0.058
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17079741; hg19: chr6-118452357;