rs10487976

Variant names:

• chr7-123195971-G-C
• rs10487976
• NM_022444.4:c.99+3877C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_022444.4(SLC13A1):​c.99+3877C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 151,748 control chromosomes in the GnomAD database, including 9,638 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 0.35 (9638 hom., cov: 32)
• Consequence: SLC13A1 NM_022444.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.327
• Publications: 3 publications found

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]

SLC13A1 Gene-Disease associations (from GenCC):

• sulfation-related bone disorder

  Inheritance: AR Classification: MODERATE Submitted by: PanelApp Australia

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022444.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC13A1	NM_022444.4	MANE Select	c.99+3877C>G		intron	N/A	NP_071889.2
	SLC13A1	NM_001324400.1		c.-775+3877C>G		intron	N/A	NP_001311329.1	Q2NKK0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC13A1	ENST00000194130.7	TSL:1 MANE Select	c.99+3877C>G		intron	N/A	ENSP00000194130.2	Q9BZW2
	SLC13A1	ENST00000439260.5	TSL:1	n.99+3877C>G		intron	N/A	ENSP00000401417.1	F8WEM4
	SLC13A1	ENST00000954470.1		c.99+3877C>G		intron	N/A	ENSP00000624529.1

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52630 AN: 151630 Hom.: 9631 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.347 AC: 52646 AN: 151748 Hom.: 9638 Cov.: 32 AF XY: 0.352 AC XY: 26120 AN XY: 74142

African (AFR) AF: 0.223 AC: 9224 AN: 41406

American (AMR) AF: 0.391 AC: 5945 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.442 AC: 1534 AN: 3472

East Asian (EAS) AF: 0.371 AC: 1898 AN: 5120

South Asian (SAS) AF: 0.408 AC: 1956 AN: 4796

European-Finnish (FIN) AF: 0.449 AC: 4733 AN: 10538

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.386 AC: 26176 AN: 67882

Other (OTH) AF: 0.334 AC: 704 AN: 2108

Alfa AF: 0.383 Hom.: 1437

Bravo AF: 0.337

Asia WGS AF: 0.345 AC: 1192 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.2
DANN	Benign	0.76
PhyloP100		-0.33
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10487976; hg19: chr7-122836025;