rs6886922

Variant names:

• chr5-139382020-G-A
• rs6886922
• NM_005847.5:c.180C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-139382020-G-A
• chr5-139382020-G-C
• chr5-139382020-G-T

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_Moderate BP7 BA1

The ENST00000348729.8(SLC23A1):​c.180C>T​(p.Ile60Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0205 in 1,608,984 control chromosomes in the GnomAD database, including 607 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 0.034 (144 hom., cov: 31)
  • Exomes 𝑓: 0.019 (463 hom.)
• Consequence: SLC23A1 ENST00000348729.8 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.511
• Publications: 13 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 -11 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BP7: Synonymous conserved (PhyloP=-0.511 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0694 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000348729.8. 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
	SLC23A1	NM_005847.5	MANE Select	c.180C>T	p.Ile60Ile	synonymous	Exon 3 of 15	NP_005838.3
	SLC23A1	NM_152685.4		c.180C>T	p.Ile60Ile	synonymous	Exon 3 of 15	NP_689898.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC23A1	ENST00000348729.8	TSL:1 MANE Select	c.180C>T	p.Ile60Ile	synonymous	Exon 3 of 15	ENSP00000302701.4
	SLC23A1	ENST00000353963.7	TSL:1	c.180C>T	p.Ile60Ile	synonymous	Exon 3 of 15	ENSP00000302851.5
	SLC23A1	ENST00000508270.1	TSL:3	c.402C>T	p.Ile134Ile	synonymous	Exon 4 of 4	ENSP00000427271.1

Frequencies

GnomAD3 genomes AF: 0.0343 AC: 5217 AN: 152134 Hom.: 143 Cov.: 31

Gnomad AFR AF: 0.0717

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0317

Gnomad ASJ AF: 0.0865

Gnomad EAS AF: 0.0264

Gnomad SAS AF: 0.0141

Gnomad FIN AF: 0.00603

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0165

Gnomad OTH AF: 0.0335

GnomAD2 exomes AF: 0.0246 AC: 5915 AN: 240448 AF XY: 0.0235

Gnomad AFR exome AF: 0.0735

Gnomad AMR exome AF: 0.0278

Gnomad ASJ exome AF: 0.0871

Gnomad EAS exome AF: 0.0240

Gnomad FIN exome AF: 0.00560

Gnomad NFE exome AF: 0.0162

Gnomad OTH exome AF: 0.0307

GnomAD4 exome AF: 0.0190 AC: 27743 AN: 1456732 Hom.: 463 Cov.: 32 AF XY: 0.0191 AC XY: 13815 AN XY: 724030

African (AFR) AF: 0.0697 AC: 2330 AN: 33412

American (AMR) AF: 0.0285 AC: 1255 AN: 43984

Ashkenazi Jewish (ASJ) AF: 0.0889 AC: 2318 AN: 26066

East Asian (EAS) AF: 0.0289 AC: 1142 AN: 39506

South Asian (SAS) AF: 0.0181 AC: 1540 AN: 85106

European-Finnish (FIN) AF: 0.00558 AC: 296 AN: 53046

Middle Eastern (MID) AF: 0.0329 AC: 188 AN: 5706

European-Non Finnish (NFE) AF: 0.0154 AC: 17101 AN: 1109724

Other (OTH) AF: 0.0261 AC: 1573 AN: 60182

GnomAD4 genome AF: 0.0343 AC: 5222 AN: 152252 Hom.: 144 Cov.: 31 AF XY: 0.0345 AC XY: 2568 AN XY: 74442

African (AFR) AF: 0.0715 AC: 2970 AN: 41530

American (AMR) AF: 0.0316 AC: 484 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0865 AC: 300 AN: 3470

East Asian (EAS) AF: 0.0259 AC: 134 AN: 5174

South Asian (SAS) AF: 0.0141 AC: 68 AN: 4834

European-Finnish (FIN) AF: 0.00603 AC: 64 AN: 10606

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0165 AC: 1120 AN: 68010

Other (OTH) AF: 0.0364 AC: 77 AN: 2114

Alfa AF: 0.0304 Hom.: 50

Bravo AF: 0.0382

Asia WGS AF: 0.0250 AC: 87 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	7.5
DANN	Benign	0.81
PhyloP100		-0.51
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: rs6886922; hg19: chr5-138717709;