rs4727963

Positions:

• chr7-123119926-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.1351-684G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 151,762 control chromosomes in the GnomAD database, including 13,987 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 0.43 (13987 hom., cov: 32)
• Consequence: SLC13A1 NM_022444.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.882

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC13A1	NM_022444.4	c.1351-684G>A		intron_variant		ENST00000194130.7	NP_071889.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC13A1	ENST00000194130.7	c.1351-684G>A		intron_variant		1	NM_022444.4	ENSP00000194130	P1
SLC13A1	ENST00000439260.5	c.*1729-684G>A		intron_variant, NMD_transcript_variant		1		ENSP00000401417
SLC13A1	ENST00000539873.1	c.*1018-684G>A		intron_variant		5		ENSP00000441309
SLC13A1	ENST00000427975.5	c.*1294-684G>A		intron_variant, NMD_transcript_variant		5		ENSP00000388403

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64827 AN: 151642 Hom.: 13981 Cov.: 32

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.392

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.427 AC: 64852 AN: 151762 Hom.: 13987 Cov.: 32 AF XY: 0.426 AC XY: 31583 AN XY: 74170

Gnomad4 AFR AF: 0.442

Gnomad4 AMR AF: 0.480

Gnomad4 ASJ AF: 0.487

Gnomad4 EAS AF: 0.339

Gnomad4 SAS AF: 0.468

Gnomad4 FIN AF: 0.371

Gnomad4 NFE AF: 0.417

Gnomad4 OTH AF: 0.415

Alfa AF: 0.423 Hom.: 18987

Bravo AF: 0.436

Asia WGS AF: 0.397 AC: 1379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.32
DANN	Benign	0.45

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: rs4727963; hg19: chr7-122759980;