7-123185902-C-T

Variant names:

• chr7-123185902-C-T
• rs10253693
• NM_022444.4:c.100-4801G>A

Variant summary

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

The NM_022444.4(SLC13A1):​c.100-4801G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 151,692 control chromosomes in the GnomAD database, including 17,048 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 0.47 (17048 hom., cov: 31)
• Consequence: SLC13A1 NM_022444.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.738
• Publications: 6 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.571 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.100-4801G>A		intron	N/A	NP_071889.2
	SLC13A1	NM_001324400.1		c.-619+4556G>A		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.100-4801G>A		intron	N/A	ENSP00000194130.2	Q9BZW2
	SLC13A1	ENST00000439260.5	TSL:1	n.*132+4556G>A		intron	N/A	ENSP00000401417.1	F8WEM4
	SLC13A1	ENST00000954470.1		c.100-4801G>A		intron	N/A	ENSP00000624529.1

Frequencies

GnomAD3 genomes AF: 0.468 AC: 70910 AN: 151574 Hom.: 17016 Cov.: 31

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.468 AC: 70991 AN: 151692 Hom.: 17048 Cov.: 31 AF XY: 0.469 AC XY: 34747 AN XY: 74138

African (AFR) AF: 0.577 AC: 23871 AN: 41378

American (AMR) AF: 0.446 AC: 6797 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.461 AC: 1596 AN: 3464

East Asian (EAS) AF: 0.402 AC: 2061 AN: 5132

South Asian (SAS) AF: 0.410 AC: 1973 AN: 4814

European-Finnish (FIN) AF: 0.471 AC: 4958 AN: 10530

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.417 AC: 28286 AN: 67818

Other (OTH) AF: 0.442 AC: 931 AN: 2108

Alfa AF: 0.433 Hom.: 38340

Bravo AF: 0.472

Asia WGS AF: 0.389 AC: 1352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.9
DANN	Benign	0.61
PhyloP100		0.74
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: rs10253693; hg19: chr7-122825956;