chr7-123119926-C-T

Variant names:

• chr7-123119926-C-T
• rs4727963
• NM_022444.4:c.1351-684G>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.1351-684G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 151,762 control chromosomes in the GnomAD database, including 13,987 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 0.43 (13987 hom., cov: 32)
• Consequence: SLC13A1 NM_022444.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.882
• 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.471 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC13A1	NM_022444.4	MANE Select	c.1351-684G>A		intron	N/A	NP_071889.2
	SLC13A1	NM_001324400.1		c.979-684G>A		intron	N/A	NP_001311329.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC13A1	ENST00000194130.7	TSL:1 MANE Select	c.1351-684G>A		intron	N/A	ENSP00000194130.2
	SLC13A1	ENST00000439260.5	TSL:1	n.*1729-684G>A		intron	N/A	ENSP00000401417.1
	SLC13A1	ENST00000539873.1	TSL:5	c.*1018-684G>A		intron	N/A	ENSP00000441309.1

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64827 AN: 151642 Hom.: 13981 Cov.: 32

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.392

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.427 AC: 64852 AN: 151762 Hom.: 13987 Cov.: 32 AF XY: 0.426 AC XY: 31583 AN XY: 74170

African (AFR) AF: 0.442 AC: 18321 AN: 41414

American (AMR) AF: 0.480 AC: 7304 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 1682 AN: 3456

East Asian (EAS) AF: 0.339 AC: 1752 AN: 5168

South Asian (SAS) AF: 0.468 AC: 2259 AN: 4822

European-Finnish (FIN) AF: 0.371 AC: 3906 AN: 10538

Middle Eastern (MID) AF: 0.425 AC: 124 AN: 292

European-Non Finnish (NFE) AF: 0.417 AC: 28274 AN: 67850

Other (OTH) AF: 0.415 AC: 873 AN: 2104

Alfa AF: 0.425 Hom.: 26460

Bravo AF: 0.436

Asia WGS AF: 0.397 AC: 1379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.32
DANN	Benign	0.45
PhyloP100		-0.88
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: rs4727963; hg19: chr7-122759980;