rs2204295

chr7-123198036-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_022444.4(SLC13A1):c.99+1812C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 151,816 control chromosomes in the GnomAD database, including 12,242 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 0.40 (12242 hom., cov: 32)
• Consequence: SLC13A1 NM_022444.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.776

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC13A1	NM_022444.4	c.99+1812C>G		intron_variant		ENST00000194130.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC13A1	ENST00000194130.7	c.99+1812C>G		intron_variant		1	NM_022444.4	P1
SLC13A1	ENST00000439260.5	c.99+1812C>G		intron_variant, NMD_transcript_variant		1
SLC13A1	ENST00000427975.5	c.99+1812C>G		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60704 AN: 151698 Hom.: 12230 Cov.: 32

Gnomad AFR AF: 0.432

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.400 AC: 60749 AN: 151816 Hom.: 12242 Cov.: 32 AF XY: 0.403 AC XY: 29867 AN XY: 74172

Gnomad4 AFR AF: 0.432

Gnomad4 AMR AF: 0.409

Gnomad4 ASJ AF: 0.438

Gnomad4 EAS AF: 0.372

Gnomad4 SAS AF: 0.398

Gnomad4 FIN AF: 0.435

Gnomad4 NFE AF: 0.374

Gnomad4 OTH AF: 0.379

Alfa AF: 0.410 Hom.: 1592

Bravo AF: 0.400

Asia WGS AF: 0.358 AC: 1244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.12
Dann	Benign	0.67

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

Publications

LitVar

Other links and lift over

dbSNP: rs2204295; hg19: chr7-122838090;