rs12706494

chr7-123132978-A-Gchr7-123132978-A-T

Variant summary

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

The NM_022444.4(SLC13A1):c.932+1432T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 152,080 control chromosomes in the GnomAD database, including 4,274 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 0.22 (4274 hom., cov: 32)
• Consequence: SLC13A1 NM_022444.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.271

Genes affected

SLC13A1 (HGNC:10916): (solute carrier family 13 member 1) The protein encoded by this gene is an apical membrane Na(+)-sulfate cotransporter involved in sulfate homeostasis in the kidney. Defects in this gene lead to many pathophysiologic problems. [provided by RefSeq, May 2016]

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 = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC13A1	NM_022444.4	c.932+1432T>C		intron_variant		ENST00000194130.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC13A1	ENST00000194130.7	c.932+1432T>C		intron_variant		1	NM_022444.4	P1
SLC13A1	ENST00000439260.5	c.*1310+1432T>C		intron_variant, NMD_transcript_variant		1
SLC13A1	ENST00000539873.1	c.*599+1432T>C		intron_variant		5
SLC13A1	ENST00000427975.5	c.*875+1432T>C		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.218 AC: 33064 AN: 151962 Hom.: 4274 Cov.: 32

Gnomad AFR AF: 0.0819

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.217 AC: 33071 AN: 152080 Hom.: 4274 Cov.: 32 AF XY: 0.219 AC XY: 16265 AN XY: 74316

Gnomad4 AFR AF: 0.0819

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.260

Gnomad4 EAS AF: 0.339

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.287

Gnomad4 NFE AF: 0.275

Gnomad4 OTH AF: 0.216

Alfa AF: 0.268 Hom.: 7983

Bravo AF: 0.205

Asia WGS AF: 0.231 AC: 800 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	2.9
Dann	Benign	0.60

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: rs12706494; hg19: chr7-122773032;