5-139383837-T-C

Variant names:

• chr5-139383837-T-C
• rs10063949
• ENST00000508270.1:c.196+521A>G

Variant summary

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

The ENST00000508270.1(SLC23A1):​c.196+521A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.482 in 152,184 control chromosomes in the GnomAD database, including 20,274 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 0.48 (20274 hom., cov: 32)
• Consequence: SLC23A1 ENST00000508270.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.523
• Publications: 28 publications found

Genes affected

SLC23A1 (HGNC:10974): (solute carrier family 23 member 1) The absorption of vitamin C into the body and its distribution to organs requires two sodium-dependent vitamin C transporters. This gene encodes one of the two transporters. The encoded protein is active in bulk vitamin C transport involving epithelial surfaces. Previously, this gene had an official symbol of SLC23A2. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.746 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC23A1	XM_005272148.4	c.379+521A>G		intron_variant	Intron 1 of 15		XP_005272205.4
SLC23A1	XM_011543765.3	c.379+521A>G		intron_variant	Intron 1 of 15		XP_011542067.2
SLC23A1	XM_047417955.1	c.379+521A>G		intron_variant	Intron 1 of 14		XP_047273911.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC23A1	ENST00000508270.1	c.196+521A>G		intron_variant	Intron 1 of 3	3		ENSP00000427271.1

Frequencies

GnomAD3 genomes AF: 0.482 AC: 73230 AN: 152066 Hom.: 20243 Cov.: 32

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.684

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.470

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

GnomAD4 genome AF: 0.482 AC: 73323 AN: 152184 Hom.: 20274 Cov.: 32 AF XY: 0.484 AC XY: 36014 AN XY: 74388

African (AFR) AF: 0.753 AC: 31280 AN: 41520

American (AMR) AF: 0.452 AC: 6917 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.460 AC: 1596 AN: 3470

East Asian (EAS) AF: 0.684 AC: 3532 AN: 5162

South Asian (SAS) AF: 0.446 AC: 2154 AN: 4832

European-Finnish (FIN) AF: 0.332 AC: 3521 AN: 10590

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.336 AC: 22824 AN: 68002

Other (OTH) AF: 0.473 AC: 1000 AN: 2112

Alfa AF: 0.395 Hom.: 34047

Bravo AF: 0.501

Asia WGS AF: 0.579 AC: 2014 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.1
DANN	Benign	0.71
PhyloP100		0.52

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10063949; hg19: chr5-138719526;