7-123134675-C-T

Variant names:

• chr7-123134675-C-T
• rs2470984
• NM_022444.4:c.813-146G>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_022444.4(SLC13A1):​c.813-146G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000023 in 434,536 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0000023 (0 hom.)
• Consequence: SLC13A1 NM_022444.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.345
• Publications: 4 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

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.813-146G>A		intron	N/A	NP_071889.2
	SLC13A1	NM_001324400.1		c.441-146G>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.813-146G>A		intron	N/A	ENSP00000194130.2	Q9BZW2
	SLC13A1	ENST00000439260.5	TSL:1	n.*1191-146G>A		intron	N/A	ENSP00000401417.1	F8WEM4
	SLC13A1	ENST00000954470.1		c.813-146G>A		intron	N/A	ENSP00000624529.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 0.00000230 AC: 1 AN: 434536 Hom.: 0 AF XY: 0.00000447 AC XY: 1 AN XY: 223712

African (AFR) AF: 0.00 AC: 0 AN: 11044

American (AMR) AF: 0.00 AC: 0 AN: 13000

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 11290

East Asian (EAS) AF: 0.0000370 AC: 1 AN: 27040

South Asian (SAS) AF: 0.00 AC: 0 AN: 25458

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 29212

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2838

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 291102

Other (OTH) AF: 0.00 AC: 0 AN: 23552

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 12165

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.41
DANN	Benign	0.20
PhyloP100		-0.34

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2470984; hg19: chr7-122774729;