rs12452028

chr17-80238432-G-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC26A11	NM_001166347.2	c.985+838G>C		intron_variant		ENST00000361193.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC26A11	ENST00000361193.8	c.985+838G>C		intron_variant		1	NM_001166347.2	P1

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

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.368

Gnomad4 ASJ AF: 0.303

Gnomad4 EAS AF: 0.596

Gnomad4 SAS AF: 0.430

Gnomad4 FIN AF: 0.338

Gnomad4 NFE AF: 0.371

Gnomad4 OTH AF: 0.316

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.90
Dann	Benign	0.43

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: rs12452028; hg19: chr17-78212231;