rs4946331

Positions:

• chr6-118244208-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_001029858.4(SLC35F1):​c.477+8572T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0137 in 152,368 control chromosomes in the GnomAD database, including 36 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 0.014 (36 hom., cov: 33)
• Consequence: SLC35F1 NM_001029858.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.15

Genes affected

SLC35F1 (HGNC:21483): (solute carrier family 35 member F1) 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=-0.98).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0137 (2093/152368) while in subpopulation AFR AF= 0.0359 (1495/41600). AF 95% confidence interval is 0.0344. There are 36 homozygotes in gnomad4. There are 1026 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 36 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC35F1	NM_001029858.4	c.477+8572T>C		intron_variant		ENST00000360388.9
SLC35F1	NM_001415931.1	c.477+8572T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC35F1	ENST00000360388.9	c.477+8572T>C		intron_variant		1	NM_001029858.4	A2
SLC35F1	ENST00000621341.1	c.300+8572T>C		intron_variant		5		P2

Frequencies

GnomAD3 genomes AF: 0.0137 AC: 2091 AN: 152250 Hom.: 36 Cov.: 33

Gnomad AFR AF: 0.0359

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0181

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0202

Gnomad SAS AF: 0.00165

Gnomad FIN AF: 0.00809

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00134

Gnomad OTH AF: 0.0129

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

GnomAD4 genome AF: 0.0137 AC: 2093 AN: 152368 Hom.: 36 Cov.: 33 AF XY: 0.0138 AC XY: 1026 AN XY: 74516

Gnomad4 AFR AF: 0.0359

Gnomad4 AMR AF: 0.0180

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.0202

Gnomad4 SAS AF: 0.00166

Gnomad4 FIN AF: 0.00809

Gnomad4 NFE AF: 0.00134

Gnomad4 OTH AF: 0.0128

Alfa AF: 0.00409 Hom.: 10

Bravo AF: 0.0159

Asia WGS AF: 0.00982 AC: 35 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.15
DANN	Benign	0.46

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: rs4946331; hg19: chr6-118565371;