6-118252898-G-A

Variant names:

• chr6-118252898-G-A
• rs281868
• NM_001029858.4:c.478-14097G>A

Variant summary

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

The NM_001029858.4(SLC35F1):​c.478-14097G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 151,870 control chromosomes in the GnomAD database, including 15,892 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 0.45 (15892 hom., cov: 31)
• Consequence: SLC35F1 NM_001029858.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0560
• Publications: 33 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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.492 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.478-14097G>A		intron	N/A	NP_001025029.2
	SLC35F1	NM_001415931.1		c.478-14097G>A		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.478-14097G>A		intron	N/A	ENSP00000353557.4
	SLC35F1	ENST00000621341.1	TSL:5	c.301-14097G>A		intron	N/A	ENSP00000484738.1

Frequencies

GnomAD3 genomes AF: 0.454 AC: 68890 AN: 151752 Hom.: 15888 Cov.: 31

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.454 AC: 68935 AN: 151870 Hom.: 15892 Cov.: 31 AF XY: 0.449 AC XY: 33339 AN XY: 74254

African (AFR) AF: 0.438 AC: 18133 AN: 41410

American (AMR) AF: 0.336 AC: 5137 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.491 AC: 1704 AN: 3470

East Asian (EAS) AF: 0.267 AC: 1373 AN: 5144

South Asian (SAS) AF: 0.461 AC: 2216 AN: 4806

European-Finnish (FIN) AF: 0.478 AC: 5045 AN: 10550

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 33732 AN: 67896

Other (OTH) AF: 0.439 AC: 927 AN: 2110

Alfa AF: 0.477 Hom.: 61947

Bravo AF: 0.442

Asia WGS AF: 0.382 AC: 1329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.2
DANN	Benign	0.29
PhyloP100		-0.056
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: rs281868; hg19: chr6-118574061; COSMIC: COSV64509629;