NM_022444.4:c.932+1432T>C

Variant names:

• chr7-123132978-A-G
• rs12706494
• NM_022444.4:c.932+1432T>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.932+1432T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 152,080 control chromosomes in the GnomAD database, including 4,274 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 0.22 (4274 hom., cov: 32)
• Consequence: SLC13A1 NM_022444.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.271
• 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC13A1	NM_022444.4	c.932+1432T>C		intron_variant	Intron 8 of 14	ENST00000194130.7	NP_071889.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC13A1	ENST00000194130.7	c.932+1432T>C		intron_variant	Intron 8 of 14	1	NM_022444.4	ENSP00000194130.2
SLC13A1	ENST00000439260.5	n.*1310+1432T>C		intron_variant	Intron 11 of 17	1		ENSP00000401417.1
SLC13A1	ENST00000539873.1	c.*599+1432T>C		intron_variant	Intron 9 of 15	5		ENSP00000441309.1
SLC13A1	ENST00000427975.5	n.*875+1432T>C		intron_variant	Intron 9 of 15	5		ENSP00000388403.1

Frequencies

GnomAD3 genomes AF: 0.218 AC: 33064 AN: 151962 Hom.: 4274 Cov.: 32

Gnomad AFR AF: 0.0819

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.217 AC: 33071 AN: 152080 Hom.: 4274 Cov.: 32 AF XY: 0.219 AC XY: 16265 AN XY: 74316

African (AFR) AF: 0.0819 AC: 3401 AN: 41506

American (AMR) AF: 0.213 AC: 3248 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.260 AC: 900 AN: 3468

East Asian (EAS) AF: 0.339 AC: 1748 AN: 5158

South Asian (SAS) AF: 0.233 AC: 1125 AN: 4830

European-Finnish (FIN) AF: 0.287 AC: 3029 AN: 10558

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.275 AC: 18709 AN: 67970

Other (OTH) AF: 0.216 AC: 456 AN: 2112

Alfa AF: 0.253 Hom.: 11133

Bravo AF: 0.205

Asia WGS AF: 0.231 AC: 800 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.9
DANN	Benign	0.60
PhyloP100		0.27
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: rs12706494; hg19: chr7-122773032;