rs10483693

Positions:

• chr14-57751705-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001306087.2(SLC35F4):​c.103+114018T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 152,212 control chromosomes in the GnomAD database, including 2,887 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 0.18 (2887 hom., cov: 32)
• Consequence: SLC35F4 NM_001306087.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.590

Genes affected

SLC35F4 (HGNC:19845): (solute carrier family 35 member F4) 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.26 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC35F4	NM_001306087.2	c.103+114018T>C		intron_variant		ENST00000556826.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC35F4	ENST00000556826.6	c.103+114018T>C		intron_variant		5	NM_001306087.2	P1
SLC35F4	ENST00000556568.1	n.283-147450T>C		intron_variant, non_coding_transcript_variant		4
SLC35F4	ENST00000557430.1	n.96+47707T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.184 AC: 27995 AN: 152094 Hom.: 2886 Cov.: 32

Gnomad AFR AF: 0.0908

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.184 AC: 27997 AN: 152212 Hom.: 2887 Cov.: 32 AF XY: 0.183 AC XY: 13610 AN XY: 74420

Gnomad4 AFR AF: 0.0909

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.238

Gnomad4 EAS AF: 0.178

Gnomad4 SAS AF: 0.272

Gnomad4 FIN AF: 0.209

Gnomad4 NFE AF: 0.226

Gnomad4 OTH AF: 0.207

Alfa AF: 0.195 Hom.: 338

Bravo AF: 0.178

Asia WGS AF: 0.200 AC: 695 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	7.6
DANN	Benign	0.80

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: rs10483693; hg19: chr14-58218423;