rs12452028

Variant names:

• chr17-80238432-G-C
• rs12452028
• NM_001166347.2:c.985+838G>C

Variant summary

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

The NM_001166347.2(SLC26A11):​c.985+838G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 152,104 control chromosomes in the GnomAD database, including 8,531 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 0.31 (8531 hom., cov: 32)
• Consequence: SLC26A11 NM_001166347.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200
• Publications: 1 publications found

Genes affected

SLC26A11 (HGNC:14471): (solute carrier family 26 member 11) This gene encodes a member of the solute linked carrier 26 family of anion exchangers. Members of this family of proteins are essential for numerous cellular functions including homeostasis and intracellular electrolyte balance. The encoded protein is a sodium independent sulfate transporter that is sensitive to the anion exchanger inhibitor 4,4'-diisothiocyanostilbene-2,2'-disulfonic acid. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Oct 2009]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001166347.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC26A11	NM_001166347.2	MANE Select	c.985+838G>C		intron	N/A	NP_001159819.1	Q86WA9
	SLC26A11	NM_001166348.2		c.985+838G>C		intron	N/A	NP_001159820.1	Q86WA9
	SLC26A11	NM_001166349.2		c.985+838G>C		intron	N/A	NP_001159821.1	Q86WA9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC26A11	ENST00000361193.8	TSL:1 MANE Select	c.985+838G>C		intron	N/A	ENSP00000355384.3	Q86WA9
	SLC26A11	ENST00000546047.7	TSL:1	c.985+838G>C		intron	N/A	ENSP00000440724.2	Q86WA9
	SLC26A11	ENST00000572725.5	TSL:1	c.985+838G>C		intron	N/A	ENSP00000459470.1	Q86WA9

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47622 AN: 151986 Hom.: 8528 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.596

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.313 AC: 47628 AN: 152104 Hom.: 8531 Cov.: 32 AF XY: 0.316 AC XY: 23511 AN XY: 74350

African (AFR) AF: 0.144 AC: 5970 AN: 41482

American (AMR) AF: 0.368 AC: 5622 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1053 AN: 3472

East Asian (EAS) AF: 0.596 AC: 3084 AN: 5172

South Asian (SAS) AF: 0.430 AC: 2078 AN: 4830

European-Finnish (FIN) AF: 0.338 AC: 3577 AN: 10568

Middle Eastern (MID) AF: 0.291 AC: 85 AN: 292

European-Non Finnish (NFE) AF: 0.371 AC: 25203 AN: 67986

Other (OTH) AF: 0.316 AC: 668 AN: 2112

Alfa AF: 0.335 Hom.: 1149

Bravo AF: 0.305

Asia WGS AF: 0.484 AC: 1682 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.90
DANN	Benign	0.43
PhyloP100		0.0020
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: rs12452028; hg19: chr17-78212231;