rs10483693

Variant names:

• chr14-57751705-A-G
• rs10483693
• NM_001306087.2:c.103+114018T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SLC35F4	NM_001306087.2	c.103+114018T>C		intron_variant	Intron 1 of 7	ENST00000556826.6	NP_001293016.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC35F4	ENST00000556826.6	c.103+114018T>C		intron_variant	Intron 1 of 7	5	NM_001306087.2	ENSP00000452086.1
SLC35F4	ENST00000556568.1	n.283-147450T>C		intron_variant	Intron 1 of 1	4
SLC35F4	ENST00000557430.1	n.96+47707T>C		intron_variant	Intron 1 of 3	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

African (AFR) AF: 0.0909 AC: 3779 AN: 41556

American (AMR) AF: 0.178 AC: 2718 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 824 AN: 3466

East Asian (EAS) AF: 0.178 AC: 921 AN: 5182

South Asian (SAS) AF: 0.272 AC: 1309 AN: 4816

European-Finnish (FIN) AF: 0.209 AC: 2210 AN: 10584

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.226 AC: 15400 AN: 68002

Other (OTH) AF: 0.207 AC: 438 AN: 2112

Alfa AF: 0.190 Hom.: 343

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
PhyloP100		0.59
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: rs10483693; hg19: chr14-58218423;