chr7-123122485-G-A

Variant names:

• chr7-123122485-G-A
• rs10255262
• NM_022444.4:c.1350+641C>T

Variant summary

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

The NM_022444.4(SLC13A1):​c.1350+641C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 151,964 control chromosomes in the GnomAD database, including 4,844 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 0.23 (4844 hom., cov: 32)
• Consequence: SLC13A1 NM_022444.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.293
• Publications: 5 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.332 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.1350+641C>T		intron	N/A	NP_071889.2
	SLC13A1	NM_001324400.1		c.978+641C>T		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.1350+641C>T		intron	N/A	ENSP00000194130.2
	SLC13A1	ENST00000439260.5	TSL:1	n.*1728+641C>T		intron	N/A	ENSP00000401417.1
	SLC13A1	ENST00000539873.1	TSL:5	c.*1017+641C>T		intron	N/A	ENSP00000441309.1

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35534 AN: 151846 Hom.: 4844 Cov.: 32

Gnomad AFR AF: 0.0968

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.234 AC: 35539 AN: 151964 Hom.: 4844 Cov.: 32 AF XY: 0.234 AC XY: 17383 AN XY: 74264

African (AFR) AF: 0.0969 AC: 4023 AN: 41520

American (AMR) AF: 0.224 AC: 3419 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 928 AN: 3464

East Asian (EAS) AF: 0.346 AC: 1781 AN: 5150

South Asian (SAS) AF: 0.247 AC: 1191 AN: 4814

European-Finnish (FIN) AF: 0.297 AC: 3127 AN: 10546

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20091 AN: 67914

Other (OTH) AF: 0.239 AC: 505 AN: 2112

Alfa AF: 0.282 Hom.: 9230

Bravo AF: 0.222

Asia WGS AF: 0.240 AC: 833 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.85
DANN	Benign	0.35
PhyloP100		-0.29
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: rs10255262; hg19: chr7-122762539;