1-205930467-T-C

Position:

• chr1-205930467-T-C

Variant summary

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

The NM_052934.4(SLC26A9):​c.553-411A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 152,024 control chromosomes in the GnomAD database, including 11,545 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 0.38 (11545 hom., cov: 32)
• Consequence: SLC26A9 NM_052934.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160

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=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC26A9	NM_052934.4	c.553-411A>G		intron_variant		ENST00000367135.8	NP_443166.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC26A9	ENST00000367135.8	c.553-411A>G		intron_variant		1	NM_052934.4	ENSP00000356103.3
SLC26A9	ENST00000340781.8	c.553-411A>G		intron_variant		1		ENSP00000341682.4
SLC26A9	ENST00000367134.2	c.553-411A>G		intron_variant		5		ENSP00000356102.2

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57385 AN: 151906 Hom.: 11543 Cov.: 32

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.378 AC: 57401 AN: 152024 Hom.: 11545 Cov.: 32 AF XY: 0.386 AC XY: 28642 AN XY: 74292

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.499

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.273

Gnomad4 SAS AF: 0.506

Gnomad4 FIN AF: 0.449

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.412

Alfa AF: 0.398 Hom.: 8253

Bravo AF: 0.373

Asia WGS AF: 0.389 AC: 1348 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	2.8
DANN	Benign	0.66

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: rs7512462; hg19: chr1-205899595;