6-118181700-G-C

Variant names:

• chr6-118181700-G-C
• rs176168
• NM_001029858.4:c.349+27080G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001029858.4(SLC35F1):​c.349+27080G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0417 in 151,754 control chromosomes in the GnomAD database, including 259 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 0.042 (259 hom., cov: 32)
• Consequence: SLC35F1 NM_001029858.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 0 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.102 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.349+27080G>C		intron	N/A	NP_001025029.2
	SLC35F1	NM_001415931.1		c.349+27080G>C		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.349+27080G>C		intron	N/A	ENSP00000353557.4
	SLC35F1	ENST00000621341.1	TSL:5	c.172+27080G>C		intron	N/A	ENSP00000484738.1

Frequencies

GnomAD3 genomes AF: 0.0417 AC: 6330 AN: 151636 Hom.: 260 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0231

Gnomad ASJ AF: 0.0318

Gnomad EAS AF: 0.0182

Gnomad SAS AF: 0.0553

Gnomad FIN AF: 0.0317

Gnomad MID AF: 0.0224

Gnomad NFE AF: 0.0110

Gnomad OTH AF: 0.0442

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

GnomAD4 genome AF: 0.0417 AC: 6335 AN: 151754 Hom.: 259 Cov.: 32 AF XY: 0.0418 AC XY: 3101 AN XY: 74134

African (AFR) AF: 0.105 AC: 4336 AN: 41372

American (AMR) AF: 0.0230 AC: 351 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.0318 AC: 110 AN: 3460

East Asian (EAS) AF: 0.0183 AC: 94 AN: 5150

South Asian (SAS) AF: 0.0549 AC: 264 AN: 4806

European-Finnish (FIN) AF: 0.0317 AC: 334 AN: 10538

Middle Eastern (MID) AF: 0.0241 AC: 7 AN: 290

European-Non Finnish (NFE) AF: 0.0110 AC: 747 AN: 67878

Other (OTH) AF: 0.0438 AC: 92 AN: 2102

Alfa AF: 0.0100 Hom.: 2

Bravo AF: 0.0426

Asia WGS AF: 0.0540 AC: 189 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.52
PhyloP100		0.31
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: rs176168; hg19: chr6-118502863;