7-123167990-C-G

Variant names:

• chr7-123167990-C-G
• rs2204290
• NM_022444.4:c.660+384G>C

Variant summary

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

The NM_022444.4(SLC13A1):​c.660+384G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 151,834 control chromosomes in the GnomAD database, including 5,049 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 0.25 (5049 hom., cov: 31)
• Consequence: SLC13A1 NM_022444.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149
• Publications: 2 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.309 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.660+384G>C		intron	N/A	NP_071889.2
	SLC13A1	NM_001324400.1		c.-58+384G>C		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.660+384G>C		intron	N/A	ENSP00000194130.2	Q9BZW2
	SLC13A1	ENST00000439260.5	TSL:1	n.*693+384G>C		intron	N/A	ENSP00000401417.1	F8WEM4
	SLC13A1	ENST00000954470.1		c.660+384G>C		intron	N/A	ENSP00000624529.1

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37827 AN: 151716 Hom.: 5048 Cov.: 31

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.249 AC: 37836 AN: 151834 Hom.: 5049 Cov.: 31 AF XY: 0.249 AC XY: 18515 AN XY: 74214

African (AFR) AF: 0.170 AC: 7054 AN: 41438

American (AMR) AF: 0.232 AC: 3534 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 911 AN: 3470

East Asian (EAS) AF: 0.322 AC: 1659 AN: 5158

South Asian (SAS) AF: 0.229 AC: 1100 AN: 4808

European-Finnish (FIN) AF: 0.301 AC: 3168 AN: 10526

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.287 AC: 19500 AN: 67890

Other (OTH) AF: 0.240 AC: 507 AN: 2110

Alfa AF: 0.170 Hom.: 390

Bravo AF: 0.238

Asia WGS AF: 0.228 AC: 794 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.5
DANN	Benign	0.18
PhyloP100		-0.15
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: rs2204290; hg19: chr7-122808044; COSMIC: COSV52009149;