20-4859624-T-C

Position:

• chr20-4859624-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005116.6(SLC23A2):​c.1625-240A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 152,150 control chromosomes in the GnomAD database, including 2,070 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 0.16 (2070 hom., cov: 33)
• Consequence: SLC23A2 NM_005116.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.20

Genes affected

SLC23A2 (HGNC:10973): (solute carrier family 23 member 2) 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 required transporters and the encoded protein accounts for tissue-specific uptake of vitamin C. Previously, this gene had an official symbol of SLC23A1. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC23A2	NM_005116.6	c.1625-240A>G		intron_variant		ENST00000338244.6	NP_005107.4
SLC23A2	NM_203327.2	c.1625-240A>G		intron_variant			NP_976072.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC23A2	ENST00000338244.6	c.1625-240A>G		intron_variant		1	NM_005116.6	ENSP00000344322	P1
SLC23A2	ENST00000379333.5	c.1625-240A>G		intron_variant		1		ENSP00000368637	P1
SLC23A2	ENST00000423430.1	c.894-240A>G		intron_variant		5		ENSP00000396364

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24193 AN: 152032 Hom.: 2067 Cov.: 33

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.159 AC: 24213 AN: 152150 Hom.: 2070 Cov.: 33 AF XY: 0.159 AC XY: 11812 AN XY: 74380

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.105

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.167

Alfa AF: 0.136 Hom.: 1964

Bravo AF: 0.163

Asia WGS AF: 0.121 AC: 423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.0030
DANN	Benign	0.49

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

Publications

LitVar

Other links and lift over

dbSNP: rs6107541; hg19: chr20-4840270; COSMIC: COSV57779320;