rs89107

Positions:

• chr6-118256880-G-A
• chr6-118256880-G-T

Variant summary

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

The NM_001029858.4(SLC35F1):​c.478-10115G>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 151,914 control chromosomes in the GnomAD database, including 15,927 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 (15927 hom., cov: 31)
• Consequence: SLC35F1 NM_001029858.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.625

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.492 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC35F1	NM_001029858.4	c.478-10115G>A		intron_variant		ENST00000360388.9
SLC35F1	NM_001415931.1	c.478-10115G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC35F1	ENST00000360388.9	c.478-10115G>A		intron_variant		1	NM_001029858.4	A2
SLC35F1	ENST00000621341.1	c.301-10115G>A		intron_variant		5		P2

Frequencies

GnomAD3 genomes AF: 0.454 AC: 68954 AN: 151796 Hom.: 15923 Cov.: 31

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.454 AC: 68999 AN: 151914 Hom.: 15927 Cov.: 31 AF XY: 0.449 AC XY: 33344 AN XY: 74246

Gnomad4 AFR AF: 0.439

Gnomad4 AMR AF: 0.336

Gnomad4 ASJ AF: 0.491

Gnomad4 EAS AF: 0.266

Gnomad4 SAS AF: 0.461

Gnomad4 FIN AF: 0.477

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.439

Alfa AF: 0.483 Hom.: 29523

Bravo AF: 0.442

Asia WGS AF: 0.382 AC: 1328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.59
DANN	Benign	0.40

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: rs89107; hg19: chr6-118578043;