NM_001306087.2:c.104-10050A>G

Variant names:

• chr14-57604174-T-C
• rs1745689
• NM_001306087.2:c.104-10050A>G

Variant summary

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

The NM_001306087.2(SLC35F4):​c.104-10050A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.712 in 152,052 control chromosomes in the GnomAD database, including 39,296 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 0.71 (39292 hom., cov: 32)
  • Exomes 𝑓: 0.90 (4 hom.)
• Consequence: SLC35F4 NM_001306087.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.99
• 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.775 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.104-10050A>G		intron	N/A	NP_001293016.1
	SLC35F4	NR_159373.2		n.406A>G		non_coding_transcript_exon	Exon 3 of 11
	SLC35F4	NM_001352014.2		c.-526A>G		5_prime_UTR	Exon 2 of 10	NP_001338943.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC35F4	ENST00000556826.6	TSL:5 MANE Select	c.104-10050A>G		intron	N/A	ENSP00000452086.1
	SLC35F4	ENST00000556568.1	TSL:4	n.364A>G		non_coding_transcript_exon	Exon 2 of 2
	SLC35F4	ENST00000557430.1	TSL:4	n.178A>G		non_coding_transcript_exon	Exon 2 of 4

Frequencies

GnomAD3 genomes AF: 0.712 AC: 108183 AN: 151924 Hom.: 39257 Cov.: 32

Gnomad AFR AF: 0.617

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.801

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.713

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.750

GnomAD4 exome AF: 0.900 AC: 9 AN: 10 Hom.: 4 Cov.: 0 AF XY: 1.00 AC XY: 8 AN XY: 8

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AF: 1.00 AC: 2 AN: 2

European-Non Finnish (NFE) AF: 1.00 AC: 6 AN: 6

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.712 AC: 108279 AN: 152042 Hom.: 39292 Cov.: 32 AF XY: 0.708 AC XY: 52572 AN XY: 74298

African (AFR) AF: 0.617 AC: 25569 AN: 41422

American (AMR) AF: 0.771 AC: 11775 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.801 AC: 2779 AN: 3470

East Asian (EAS) AF: 0.346 AC: 1790 AN: 5172

South Asian (SAS) AF: 0.672 AC: 3231 AN: 4808

European-Finnish (FIN) AF: 0.713 AC: 7536 AN: 10570

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.781 AC: 53107 AN: 68000

Other (OTH) AF: 0.750 AC: 1586 AN: 2114

Alfa AF: 0.742 Hom.: 7361

Bravo AF: 0.713

Asia WGS AF: 0.562 AC: 1955 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	0.048
DANN	Benign	0.37
PhyloP100		-4.0
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: rs1745689; hg19: chr14-58070892;