chr14-57734007-A-G

Variant names:

• chr14-57734007-A-G
• rs1092015
• NM_001306087.2:c.103+131716T>C

Variant summary

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

The NM_001306087.2(SLC35F4):​c.103+131716T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.896 in 152,176 control chromosomes in the GnomAD database, including 62,017 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 0.90 (62017 hom., cov: 32)
• Consequence: SLC35F4 NM_001306087.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.259
• Publications: 6 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.976 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.103+131716T>C		intron	N/A	NP_001293016.1
	SLC35F4	NM_001206920.2		c.103+131716T>C		intron	N/A	NP_001193849.1
	SLC35F4	NM_001352015.3		c.94+131554T>C		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.103+131716T>C		intron	N/A	ENSP00000452086.1
	SLC35F4	ENST00000556568.1	TSL:4	n.283-129752T>C		intron	N/A
	SLC35F4	ENST00000557430.1	TSL:4	n.96+65405T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.896 AC: 136318 AN: 152058 Hom.: 61980 Cov.: 32

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.989

Gnomad AMR AF: 0.875

Gnomad ASJ AF: 0.985

Gnomad EAS AF: 0.835

Gnomad SAS AF: 0.975

Gnomad FIN AF: 0.966

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.982

Gnomad OTH AF: 0.909

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

GnomAD4 genome AF: 0.896 AC: 136405 AN: 152176 Hom.: 62017 Cov.: 32 AF XY: 0.897 AC XY: 66727 AN XY: 74402

African (AFR) AF: 0.734 AC: 30421 AN: 41452

American (AMR) AF: 0.875 AC: 13381 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.985 AC: 3420 AN: 3472

East Asian (EAS) AF: 0.835 AC: 4328 AN: 5184

South Asian (SAS) AF: 0.975 AC: 4697 AN: 4816

European-Finnish (FIN) AF: 0.966 AC: 10246 AN: 10610

Middle Eastern (MID) AF: 0.939 AC: 276 AN: 294

European-Non Finnish (NFE) AF: 0.982 AC: 66809 AN: 68028

Other (OTH) AF: 0.910 AC: 1925 AN: 2116

Alfa AF: 0.940 Hom.: 100460

Bravo AF: 0.881

Asia WGS AF: 0.899 AC: 3126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.44
DANN	Benign	0.39
PhyloP100		-0.26
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: rs1092015; hg19: chr14-58200725;