rs56993779

Positions:

• chr8-86214405-TCCGACATC-T

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP6_Moderate BP7 BA1

The NM_138817.3(SLC7A13):​c.1413_*7del variant causes a stop retained, 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 1,572,080 control chromosomes in the GnomAD database, including 20,645 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.13 (1705 hom., cov: 30)
  • Exomes 𝑓: 0.15 (18940 hom.)
• Consequence: SLC7A13 NM_138817.3 stop_retained, 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.83

Genes affected

SLC7A13 (HGNC:23092): (solute carrier family 7 member 13) Predicted to enable L-amino acid transmembrane transporter activity. Predicted to be involved in L-cystine transport; L-glutamate transmembrane transport; and aspartate transmembrane transport. Predicted to be integral component of membrane. Predicted to be active in apical plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -11 ACMG points.

• BP6: Variant 8-86214405-TCCGACATC-T is Benign according to our data. Variant chr8-86214405-TCCGACATC-T is described in ClinVar as [Benign]. Clinvar id is 1620765.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=2.83 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC7A13	NM_138817.3	c.1413_*7del		stop_retained_variant, 3_prime_UTR_variant	4/4	ENST00000297524.8
SLC7A13	XM_011516867.3	c.1386_*7del		stop_retained_variant, 3_prime_UTR_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC7A13	ENST00000297524.8	c.1413_*7del		stop_retained_variant, 3_prime_UTR_variant	4/4	1	NM_138817.3	P1
SLC7A13	ENST00000419776.2	c.*212_*219del		3_prime_UTR_variant	5/5	1

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19557 AN: 151998 Hom.: 1700 Cov.: 30

Gnomad AFR AF: 0.0562

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.149

GnomAD3 exomes AF: 0.181 AC: 42497 AN: 234406 Hom.: 4632 AF XY: 0.187 AC XY: 23905 AN XY: 127872

Gnomad AFR exome AF: 0.0555

Gnomad AMR exome AF: 0.236

Gnomad ASJ exome AF: 0.194

Gnomad EAS exome AF: 0.320

Gnomad SAS exome AF: 0.317

Gnomad FIN exome AF: 0.116

Gnomad NFE exome AF: 0.134

Gnomad OTH exome AF: 0.170

GnomAD4 exome AF: 0.150 AC: 212309 AN: 1419964 Hom.: 18940 AF XY: 0.155 AC XY: 109814 AN XY: 707404

Gnomad4 AFR exome AF: 0.0519

Gnomad4 AMR exome AF: 0.229

Gnomad4 ASJ exome AF: 0.193

Gnomad4 EAS exome AF: 0.318

Gnomad4 SAS exome AF: 0.318

Gnomad4 FIN exome AF: 0.118

Gnomad4 NFE exome AF: 0.129

Gnomad4 OTH exome AF: 0.159

GnomAD4 genome AF: 0.129 AC: 19574 AN: 152116 Hom.: 1705 Cov.: 30 AF XY: 0.132 AC XY: 9837 AN XY: 74348

Gnomad4 AFR AF: 0.0561

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.150

Alfa AF: 0.137 Hom.: 326

Bravo AF: 0.128

Asia WGS AF: 0.322 AC: 1119 AN: 3476

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

Invitae

Jan 30, 2024

- -

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: rs56993779; hg19: chr8-87226634;