chr5-139369899-A-G

Variant names:

• chr5-139369899-A-G
• rs6596471
• NM_005847.5:c.*19+2088T>C

Variant summary

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

The NM_005847.5(SLC23A1):​c.*19+2088T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 151,878 control chromosomes in the GnomAD database, including 14,468 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 0.40 (14468 hom., cov: 32)
• Consequence: SLC23A1 NM_005847.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.245
• Publications: 9 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]

PAIP2 (HGNC:17970): (poly(A) binding protein interacting protein 2) Enables translation repressor activity. Involved in negative regulation of translational initiation. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000272742 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.752 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC23A1	NM_005847.5	c.*19+2088T>C		intron_variant	Intron 14 of 14	ENST00000348729.8	NP_005838.3
PAIP2	NM_016480.5	c.*1101A>G		downstream_gene_variant		ENST00000265192.9	NP_057564.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC23A1	ENST00000348729.8	c.*19+2088T>C		intron_variant	Intron 14 of 14	1	NM_005847.5	ENSP00000302701.4
PAIP2	ENST00000265192.9	c.*1101A>G		downstream_gene_variant		1	NM_016480.5	ENSP00000265192.4

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61264 AN: 151760 Hom.: 14450 Cov.: 32

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.772

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.404 AC: 61322 AN: 151878 Hom.: 14468 Cov.: 32 AF XY: 0.410 AC XY: 30415 AN XY: 74200

African (AFR) AF: 0.619 AC: 25637 AN: 41402

American (AMR) AF: 0.381 AC: 5820 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 1023 AN: 3468

East Asian (EAS) AF: 0.772 AC: 3979 AN: 5156

South Asian (SAS) AF: 0.346 AC: 1664 AN: 4812

European-Finnish (FIN) AF: 0.342 AC: 3600 AN: 10520

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18323 AN: 67944

Other (OTH) AF: 0.381 AC: 804 AN: 2112

Alfa AF: 0.291 Hom.: 4926

Bravo AF: 0.418

Asia WGS AF: 0.552 AC: 1920 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.0
DANN	Benign	0.72
PhyloP100		-0.24
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		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: rs6596471; hg19: chr5-138705588;