chr7-123167626-T-C

Position:

• chr7-123167626-T-C

Variant summary

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

The NM_022444.4(SLC13A1):​c.660+748A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 151,916 control chromosomes in the GnomAD database, including 5,798 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 0.27 (5798 hom., cov: 31)
• Consequence: SLC13A1 NM_022444.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC13A1	NM_022444.4	c.660+748A>G		intron_variant		ENST00000194130.7	NP_071889.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC13A1	ENST00000194130.7	c.660+748A>G		intron_variant		1	NM_022444.4	ENSP00000194130	P1
SLC13A1	ENST00000439260.5	c.*693+748A>G		intron_variant, NMD_transcript_variant		1		ENSP00000401417
SLC13A1	ENST00000539873.1	c.468+748A>G		intron_variant		5		ENSP00000441309
SLC13A1	ENST00000427975.5	c.*603+748A>G		intron_variant, NMD_transcript_variant		5		ENSP00000388403

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41491 AN: 151798 Hom.: 5796 Cov.: 31

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.273 AC: 41516 AN: 151916 Hom.: 5798 Cov.: 31 AF XY: 0.272 AC XY: 20232 AN XY: 74254

Gnomad4 AFR AF: 0.254

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.301

Gnomad4 NFE AF: 0.287

Gnomad4 OTH AF: 0.259

Alfa AF: 0.284 Hom.: 10770

Bravo AF: 0.267

Asia WGS AF: 0.234 AC: 813 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.1
DANN	Benign	0.34

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: rs1343905; hg19: chr7-122807680;