rs2470984

Positions:

• chr7-123134675-C-A
• chr7-123134675-C-G
• chr7-123134675-C-T

Variant summary

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

The NM_022444.4(SLC13A1):​c.813-146G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 584,892 control chromosomes in the GnomAD database, including 28,241 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 0.36 (10476 hom., cov: 31)
  • Exomes 𝑓: 0.28 (17765 hom.)
• Consequence: SLC13A1 NM_022444.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.345

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 (AFR) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC13A1	NM_022444.4	c.813-146G>T		intron_variant		ENST00000194130.7	NP_071889.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC13A1	ENST00000194130.7	c.813-146G>T		intron_variant		1	NM_022444.4	ENSP00000194130	P1
SLC13A1	ENST00000439260.5	c.*1191-146G>T		intron_variant, NMD_transcript_variant		1		ENSP00000401417
SLC13A1	ENST00000539873.1	c.*480-146G>T		intron_variant		5		ENSP00000441309
SLC13A1	ENST00000427975.5	c.*756-146G>T		intron_variant, NMD_transcript_variant		5		ENSP00000388403

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53897 AN: 151800 Hom.: 10441 Cov.: 31

Gnomad AFR AF: 0.516

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.338

GnomAD4 exome AF: 0.276 AC: 119691 AN: 432974 Hom.: 17765 AF XY: 0.276 AC XY: 61412 AN XY: 222900

Gnomad4 AFR exome AF: 0.503

Gnomad4 AMR exome AF: 0.240

Gnomad4 ASJ exome AF: 0.230

Gnomad4 EAS exome AF: 0.255

Gnomad4 SAS exome AF: 0.244

Gnomad4 FIN exome AF: 0.310

Gnomad4 NFE exome AF: 0.270

Gnomad4 OTH exome AF: 0.301

GnomAD4 genome AF: 0.355 AC: 53991 AN: 151918 Hom.: 10476 Cov.: 31 AF XY: 0.356 AC XY: 26405 AN XY: 74232

Gnomad4 AFR AF: 0.516

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.242

Gnomad4 EAS AF: 0.293

Gnomad4 SAS AF: 0.292

Gnomad4 FIN AF: 0.334

Gnomad4 NFE AF: 0.291

Gnomad4 OTH AF: 0.347

Alfa AF: 0.289 Hom.: 8844

Bravo AF: 0.361

Asia WGS AF: 0.360 AC: 1255 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	0.32
DANN	Benign	0.35

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: rs2470984; hg19: chr7-122774729;