chr6-118297818-T-C

Variant names:

• chr6-118297818-T-C
• rs166881
• NM_001029858.4:c.1002+12480T>C

Variant summary

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

The NM_001029858.4(SLC35F1):​c.1002+12480T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 149,250 control chromosomes in the GnomAD database, including 1,364 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 0.12 (1364 hom., cov: 29)
• Consequence: SLC35F1 NM_001029858.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 4 publications found

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]

ENSG00000301363 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC35F1	NM_001029858.4	c.1002+12480T>C		intron_variant	Intron 7 of 7	ENST00000360388.9	NP_001025029.2
SLC35F1	NM_001415931.1	c.1002+12480T>C		intron_variant	Intron 7 of 8		NP_001402860.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC35F1	ENST00000360388.9	c.1002+12480T>C		intron_variant	Intron 7 of 7	1	NM_001029858.4	ENSP00000353557.4
SLC35F1	ENST00000621341.1	c.825+12480T>C		intron_variant	Intron 6 of 6	5		ENSP00000484738.1
ENSG00000301363	ENST00000778493.1	n.239+26268A>G		intron_variant	Intron 1 of 1
ENSG00000301363	ENST00000778494.1	n.166-7308A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17186 AN: 149168 Hom.: 1367 Cov.: 29

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.00330

Gnomad AMR AF: 0.0678

Gnomad ASJ AF: 0.0912

Gnomad EAS AF: 0.0246

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.0664

Gnomad MID AF: 0.0513

Gnomad NFE AF: 0.0822

Gnomad OTH AF: 0.0980

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

GnomAD4 genome AF: 0.115 AC: 17181 AN: 149250 Hom.: 1364 Cov.: 29 AF XY: 0.113 AC XY: 8245 AN XY: 72762

African (AFR) AF: 0.218 AC: 8807 AN: 40370

American (AMR) AF: 0.0677 AC: 1009 AN: 14908

Ashkenazi Jewish (ASJ) AF: 0.0912 AC: 316 AN: 3466

East Asian (EAS) AF: 0.0247 AC: 127 AN: 5138

South Asian (SAS) AF: 0.106 AC: 502 AN: 4732

European-Finnish (FIN) AF: 0.0664 AC: 649 AN: 9774

Middle Eastern (MID) AF: 0.0382 AC: 11 AN: 288

European-Non Finnish (NFE) AF: 0.0822 AC: 5559 AN: 67616

Other (OTH) AF: 0.0966 AC: 198 AN: 2050

Alfa AF: 0.0654 Hom.: 149

Bravo AF: 0.119

Asia WGS AF: 0.0600 AC: 209 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.67
PhyloP100		0.21
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: rs166881; hg19: chr6-118618981;