NM_005847.5:c.1179+109C>T

Variant names:

• chr5-139378470-G-A
• rs4257763
• NM_005847.5:c.1179+109C>T

Variant summary

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

The NM_005847.5(SLC23A1):​c.1179+109C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.616 in 1,423,780 control chromosomes in the GnomAD database, including 283,414 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 (21824 hom., cov: 32)
  • Exomes 𝑓: 0.63 (261590 hom.)
• Consequence: SLC23A1 NM_005847.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.369
• Publications: 16 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005847.5. 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.1179+109C>T		intron	N/A	NP_005838.3
	SLC23A1	NM_152685.4		c.1191+109C>T		intron	N/A	NP_689898.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC23A1	ENST00000348729.8	TSL:1 MANE Select	c.1179+109C>T		intron	N/A	ENSP00000302701.4
	SLC23A1	ENST00000353963.7	TSL:1	c.1191+109C>T		intron	N/A	ENSP00000302851.5
	SLC23A1	ENST00000504513.1	TSL:5	c.*121C>T		downstream_gene	N/A	ENSP00000422688.1

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73612 AN: 151758 Hom.: 21832 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.507

GnomAD4 exome AF: 0.631 AC: 802732 AN: 1271902 Hom.: 261590 Cov.: 19 AF XY: 0.630 AC XY: 396963 AN XY: 630114

African (AFR) AF: 0.131 AC: 3846 AN: 29312

American (AMR) AF: 0.611 AC: 20981 AN: 34366

Ashkenazi Jewish (ASJ) AF: 0.530 AC: 12184 AN: 23002

East Asian (EAS) AF: 0.318 AC: 11160 AN: 35084

South Asian (SAS) AF: 0.550 AC: 40904 AN: 74404

European-Finnish (FIN) AF: 0.670 AC: 32216 AN: 48110

Middle Eastern (MID) AF: 0.514 AC: 1943 AN: 3778

European-Non Finnish (NFE) AF: 0.668 AC: 648735 AN: 970518

Other (OTH) AF: 0.577 AC: 30763 AN: 53328

GnomAD4 genome AF: 0.485 AC: 73608 AN: 151878 Hom.: 21824 Cov.: 32 AF XY: 0.484 AC XY: 35884 AN XY: 74196

African (AFR) AF: 0.140 AC: 5805 AN: 41444

American (AMR) AF: 0.538 AC: 8220 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1856 AN: 3468

East Asian (EAS) AF: 0.278 AC: 1422 AN: 5124

South Asian (SAS) AF: 0.543 AC: 2609 AN: 4808

European-Finnish (FIN) AF: 0.669 AC: 7046 AN: 10534

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.661 AC: 44894 AN: 67906

Other (OTH) AF: 0.503 AC: 1064 AN: 2114

Alfa AF: 0.568 Hom.: 9046

Bravo AF: 0.463

Asia WGS AF: 0.386 AC: 1343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.76
DANN	Benign	0.95
PhyloP100		0.37
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs4257763; hg19: chr5-138714159;