chr19-32830869-C-G

Position:

• chr19-32830869-C-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The ENST00000023064.9(SLC7A9):​c.1400-185G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,194 control chromosomes in the GnomAD database, including 1,089 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency: Genomes: 𝑓 0.11 (1089 hom., cov: 31)
• Consequence: SLC7A9 ENST00000023064.9 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.373

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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 19-32830869-C-G is Benign according to our data. Variant chr19-32830869-C-G is described in ClinVar as [Benign]. Clinvar id is 1222556.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC7A9	NM_014270.5	c.1400-185G>C		intron_variant		ENST00000023064.9	NP_055085.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC7A9	ENST00000023064.9	c.1400-185G>C		intron_variant		1	NM_014270.5	ENSP00000023064	P1

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16270 AN: 152076 Hom.: 1091 Cov.: 31

Gnomad AFR AF: 0.0257

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.0935

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.0579

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.107 AC: 16263 AN: 152194 Hom.: 1089 Cov.: 31 AF XY: 0.106 AC XY: 7879 AN XY: 74400

Gnomad4 AFR AF: 0.0256

Gnomad4 AMR AF: 0.0933

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.0579

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.122

Alfa AF: 0.121 Hom.: 162

Bravo AF: 0.102

Asia WGS AF: 0.0690 AC: 240 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Dec 08, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.89
DANN	Benign	0.59

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: rs17272190; hg19: chr19-33321775; COSMIC: COSV50085059; COSMIC: COSV50085059;