rs1092015

chr14-57734007-A-Gchr14-57734007-A-T

Variant summary

Our verdict is Benign. Variant got -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

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 -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC35F4	NM_001306087.2	c.103+131716T>C		intron_variant		ENST00000556826.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC35F4	ENST00000556826.6	c.103+131716T>C		intron_variant		5	NM_001306087.2	P1
SLC35F4	ENST00000556568.1	n.283-129752T>C		intron_variant, non_coding_transcript_variant		4
SLC35F4	ENST00000557430.1	n.96+65405T>C		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.734

Gnomad4 AMR AF: 0.875

Gnomad4 ASJ AF: 0.985

Gnomad4 EAS AF: 0.835

Gnomad4 SAS AF: 0.975

Gnomad4 FIN AF: 0.966

Gnomad4 NFE AF: 0.982

Gnomad4 OTH AF: 0.910

Alfa AF: 0.926 Hom.: 11603

Bravo AF: 0.881

Asia WGS AF: 0.899 AC: 3126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.44
Dann	Benign	0.39

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: rs1092015; hg19: chr14-58200725;