6-118300293-G-A

Variant names:

• chr6-118300293-G-A
• rs283062
• NM_001029858.4:c.1003-13735G>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.1003-13735G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 151,954 control chromosomes in the GnomAD database, including 26,200 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 0.58 (26200 hom., cov: 32)
• Consequence: SLC35F1 NM_001029858.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.470
• Publications: 4 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]

ENSG00000301363 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC35F1	NM_001029858.4	c.1003-13735G>A		intron_variant	Intron 7 of 7	ENST00000360388.9	NP_001025029.2
SLC35F1	NM_001415931.1	c.1003-13735G>A		intron_variant	Intron 7 of 8		NP_001402860.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC35F1	ENST00000360388.9	c.1003-13735G>A		intron_variant	Intron 7 of 7	1	NM_001029858.4	ENSP00000353557.4

Frequencies

GnomAD3 genomes AF: 0.580 AC: 88092 AN: 151834 Hom.: 26182 Cov.: 32

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.580 AC: 88162 AN: 151954 Hom.: 26200 Cov.: 32 AF XY: 0.572 AC XY: 42482 AN XY: 74262

African (AFR) AF: 0.691 AC: 28641 AN: 41446

American (AMR) AF: 0.430 AC: 6559 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.538 AC: 1865 AN: 3466

East Asian (EAS) AF: 0.296 AC: 1526 AN: 5156

South Asian (SAS) AF: 0.539 AC: 2596 AN: 4816

European-Finnish (FIN) AF: 0.535 AC: 5651 AN: 10558

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.583 AC: 39632 AN: 67942

Other (OTH) AF: 0.536 AC: 1130 AN: 2110

Alfa AF: 0.564 Hom.: 4078

Bravo AF: 0.573

Asia WGS AF: 0.430 AC: 1496 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.8
DANN	Benign	0.77
PhyloP100		-0.47
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: rs283062; hg19: chr6-118621456;