19-32830811-A-AGG

Variant summary

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

The NM_014270.5(SLC7A9):c.1400-128_1400-127insCC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 751,580 control chromosomes in the GnomAD database, including 119,485 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.59 (27596 hom., cov: 0)
  • Exomes 𝑓: 0.54 (91889 hom.)
• Consequence: SLC7A9 NM_014270.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.675

Genes affected

SLC7A9 (HGNC:11067): (solute carrier family 7 member 9) This gene encodes a protein that belongs to a family of light subunits of amino acid transporters. This protein plays a role in the high-affinity and sodium-independent transport of cystine and neutral and dibasic amino acids, and appears to function in the reabsorption of cystine in the kidney tubule. Mutations in this gene cause non-type I cystinuria, a disease that leads to cystine stones in the urinary system due to impaired transport of cystine and dibasic amino acids. Alternate transcript variants, which encode the same protein, have been found for this gene. [provided by RefSeq, Jul 2011]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 19-32830811-A-AGG is Benign according to our data. Variant chr19-32830811-A-AGG is described in ClinVar as [Benign]. Clinvar id is 1295545.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.802 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC7A9	NM_014270.5	c.1400-128_1400-127insCC		intron_variant		ENST00000023064.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC7A9	ENST00000023064.9	c.1400-128_1400-127insCC		intron_variant		1	NM_014270.5	P1

Frequencies

GnomAD3 genomes AF: 0.592 AC: 89980 AN: 151924 Hom.: 27553 Cov.: 0

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.822

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.656

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.606

GnomAD4 exome AF: 0.545 AC: 326507 AN: 599538 Hom.: 91889 AF XY: 0.543 AC XY: 175029 AN XY: 322230

Gnomad4 AFR exome AF: 0.734

Gnomad4 AMR exome AF: 0.460

Gnomad4 ASJ exome AF: 0.605

Gnomad4 EAS exome AF: 0.857

Gnomad4 SAS exome AF: 0.531

Gnomad4 FIN exome AF: 0.528

Gnomad4 NFE exome AF: 0.513

Gnomad4 OTH exome AF: 0.569

GnomAD4 genome AF: 0.592 AC: 90073 AN: 152042 Hom.: 27596 Cov.: 0 AF XY: 0.592 AC XY: 43972 AN XY: 74304

Gnomad4 AFR AF: 0.734

Gnomad4 AMR AF: 0.509

Gnomad4 ASJ AF: 0.603

Gnomad4 EAS AF: 0.822

Gnomad4 SAS AF: 0.537

Gnomad4 FIN AF: 0.536

Gnomad4 NFE AF: 0.519

Gnomad4 OTH AF: 0.605

Alfa AF: 0.627 Hom.: 2825

Bravo AF: 0.600

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 20, 2019

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10645053; hg19: chr19-33321717;