14-57652478-C-T

Variant names:

• chr14-57652478-C-T
• rs10134944
• NM_001306087.2:c.104-58354G>A

Variant summary

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

The NM_001306087.2(SLC35F4):​c.104-58354G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,058 control chromosomes in the GnomAD database, including 1,461 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 0.13 (1461 hom., cov: 32)
• Consequence: SLC35F4 NM_001306087.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 9 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001306087.2. 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
	SLC35F4	NM_001306087.2	MANE Select	c.104-58354G>A		intron	N/A	NP_001293016.1
	SLC35F4	NM_001206920.2		c.104-58354G>A		intron	N/A	NP_001193849.1
	SLC35F4	NM_001352015.3		c.95-58354G>A		intron	N/A	NP_001338944.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC35F4	ENST00000556826.6	TSL:5 MANE Select	c.104-58354G>A		intron	N/A	ENSP00000452086.1
	SLC35F4	ENST00000556568.1	TSL:4	n.283-48223G>A		intron	N/A
	SLC35F4	ENST00000557430.1	TSL:4	n.97-48223G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19675 AN: 151940 Hom.: 1455 Cov.: 32

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.0967

Gnomad AMR AF: 0.0961

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0899

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.0974

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.130 AC: 19708 AN: 152058 Hom.: 1461 Cov.: 32 AF XY: 0.127 AC XY: 9458 AN XY: 74320

African (AFR) AF: 0.197 AC: 8176 AN: 41476

American (AMR) AF: 0.0962 AC: 1469 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 657 AN: 3466

East Asian (EAS) AF: 0.167 AC: 862 AN: 5152

South Asian (SAS) AF: 0.115 AC: 553 AN: 4816

European-Finnish (FIN) AF: 0.0899 AC: 953 AN: 10598

Middle Eastern (MID) AF: 0.138 AC: 40 AN: 290

European-Non Finnish (NFE) AF: 0.0974 AC: 6623 AN: 67970

Other (OTH) AF: 0.136 AC: 287 AN: 2110

Alfa AF: 0.108 Hom.: 701

Bravo AF: 0.134

Asia WGS AF: 0.169 AC: 588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.37
PhyloP100		-1.5
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: rs10134944; hg19: chr14-58119196;