chr5-139378785-G-A

Position:

• chr5-139378785-G-A

Variant summary

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

The NM_005847.5(SLC23A1):​c.1074-101C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.587 in 841,620 control chromosomes in the GnomAD database, including 155,389 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 (21694 hom., cov: 31)
  • Exomes 𝑓: 0.61 (133695 hom.)
• Consequence: SLC23A1 NM_005847.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC23A1	NM_005847.5	c.1074-101C>T		intron_variant		ENST00000348729.8	NP_005838.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC23A1	ENST00000348729.8	c.1074-101C>T		intron_variant		1	NM_005847.5	ENSP00000302701.4
SLC23A1	ENST00000353963.7	c.1086-101C>T		intron_variant		1		ENSP00000302851.5
SLC23A1	ENST00000504513.1	c.312-101C>T		intron_variant		5		ENSP00000422688.1

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73444 AN: 151898 Hom.: 21702 Cov.: 31

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.505

GnomAD4 exome AF: 0.610 AC: 420883 AN: 689602 Hom.: 133695 AF XY: 0.610 AC XY: 220508 AN XY: 361490

Gnomad4 AFR exome AF: 0.145

Gnomad4 AMR exome AF: 0.609

Gnomad4 ASJ exome AF: 0.527

Gnomad4 EAS exome AF: 0.323

Gnomad4 SAS exome AF: 0.554

Gnomad4 FIN exome AF: 0.666

Gnomad4 NFE exome AF: 0.661

Gnomad4 OTH exome AF: 0.563

GnomAD4 genome AF: 0.483 AC: 73440 AN: 152018 Hom.: 21694 Cov.: 31 AF XY: 0.482 AC XY: 35823 AN XY: 74300

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.539

Gnomad4 ASJ AF: 0.533

Gnomad4 EAS AF: 0.279

Gnomad4 SAS AF: 0.543

Gnomad4 FIN AF: 0.663

Gnomad4 NFE AF: 0.659

Gnomad4 OTH AF: 0.502

Alfa AF: 0.620 Hom.: 51108

Bravo AF: 0.462

Asia WGS AF: 0.387 AC: 1346 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	6.7
DANN	Benign	0.78

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: rs11950646; hg19: chr5-138714474; COSMIC: COSV62296133; COSMIC: COSV62296133;