rs11240594

chr1-205927107-G-A

Variant summary

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

The NM_052934.4(SLC26A9):c.1293+104C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 1,182,134 control chromosomes in the GnomAD database, including 25,944 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 0.20 (3460 hom., cov: 32)
  • Exomes 𝑓: 0.19 (22484 hom.)
• Consequence: SLC26A9 NM_052934.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.311

Genes affected

SLC26A9 (HGNC:14469): (solute carrier family 26 member 9) This gene is one member of a family of sulfate/anion transporter genes. Family members are well conserved in their genomic (number and size of exons) and protein (aa length among species) structures yet have markedly different tissue expression patterns. The product of this gene is a highly selective chloride ion channel regulated by WNK kinases. Alternative splicing results in multiple transcript variants encoding differing isoforms.[provided by RefSeq, Dec 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.552 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC26A9	NM_052934.4	c.1293+104C>T		intron_variant		ENST00000367135.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC26A9	ENST00000367135.8	c.1293+104C>T		intron_variant		1	NM_052934.4	P1
SLC26A9	ENST00000340781.8	c.1293+104C>T		intron_variant		1
SLC26A9	ENST00000367134.2	c.1293+104C>T		intron_variant		5
SLC26A9	ENST00000491127.5	n.677+104C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29952 AN: 152064 Hom.: 3456 Cov.: 32

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.569

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.215

GnomAD4 exome AF: 0.190 AC: 196055 AN: 1029952 Hom.: 22484 AF XY: 0.193 AC XY: 101502 AN XY: 527264

Gnomad4 AFR exome AF: 0.222

Gnomad4 AMR exome AF: 0.240

Gnomad4 ASJ exome AF: 0.208

Gnomad4 EAS exome AF: 0.575

Gnomad4 SAS exome AF: 0.272

Gnomad4 FIN exome AF: 0.134

Gnomad4 NFE exome AF: 0.160

Gnomad4 OTH exome AF: 0.208

GnomAD4 genome AF: 0.197 AC: 29992 AN: 152182 Hom.: 3460 Cov.: 32 AF XY: 0.199 AC XY: 14770 AN XY: 74388

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.569

Gnomad4 SAS AF: 0.271

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.213

Alfa AF: 0.182 Hom.: 6446

Bravo AF: 0.208

Asia WGS AF: 0.380 AC: 1321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.53
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: rs11240594; hg19: chr1-205896235;