7-123117451-A-AT

Position:

• chr7-123117451-A-AT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_022444.4(SLC13A1):​c.1650+19_1650+20insA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 1,608,160 control chromosomes in the GnomAD database, including 44,660 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.19 (3461 hom., cov: 27)
  • Exomes 𝑓: 0.23 (41199 hom.)
• Consequence: SLC13A1 NM_022444.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.15

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 -10 ACMG points.

• BP6: Variant 7-123117451-A-AT is Benign according to our data. Variant chr7-123117451-A-AT is described in ClinVar as [Benign]. Clinvar id is 1288300.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC13A1	NM_022444.4	c.1650+19_1650+20insA		intron_variant		ENST00000194130.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC13A1	ENST00000194130.7	c.1650+19_1650+20insA		intron_variant		1	NM_022444.4	P1
SLC13A1	ENST00000439260.5	c.*2028+19_*2028+20insA		intron_variant, NMD_transcript_variant		1
SLC13A1	ENST00000539873.1	c.*1317+19_*1317+20insA		intron_variant		5
SLC13A1	ENST00000427975.5	c.*1593+19_*1593+20insA		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28604 AN: 151838 Hom.: 3458 Cov.: 27

Gnomad AFR AF: 0.0469

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.0805

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.206

GnomAD3 exomes AF: 0.222 AC: 55291 AN: 249266 Hom.: 6967 AF XY: 0.219 AC XY: 29460 AN XY: 134758

Gnomad AFR exome AF: 0.0397

Gnomad AMR exome AF: 0.320

Gnomad ASJ exome AF: 0.305

Gnomad EAS exome AF: 0.0889

Gnomad SAS exome AF: 0.121

Gnomad FIN exome AF: 0.246

Gnomad NFE exome AF: 0.255

Gnomad OTH exome AF: 0.224

GnomAD4 exome AF: 0.232 AC: 337342 AN: 1456204 Hom.: 41199 Cov.: 31 AF XY: 0.229 AC XY: 165846 AN XY: 724584

Gnomad4 AFR exome AF: 0.0384

Gnomad4 AMR exome AF: 0.316

Gnomad4 ASJ exome AF: 0.304

Gnomad4 EAS exome AF: 0.0823

Gnomad4 SAS exome AF: 0.126

Gnomad4 FIN exome AF: 0.244

Gnomad4 NFE exome AF: 0.246

Gnomad4 OTH exome AF: 0.216

GnomAD4 genome AF: 0.188 AC: 28607 AN: 151956 Hom.: 3461 Cov.: 27 AF XY: 0.190 AC XY: 14079 AN XY: 74254

Gnomad4 AFR AF: 0.0468

Gnomad4 AMR AF: 0.282

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.0803

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.204

Alfa AF: 0.170 Hom.: 528

Bravo AF: 0.187

Asia WGS AF: 0.0960 AC: 333 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 15, 2019

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs28364221; hg19: chr7-122757505;