Variant rs56993779 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM4BP6_ModerateBA1

The NM_138817.3(SLC7A13):c.1413_*7delGATGTCGG(p.Ter471fs) variant causes a frameshift, stop lost 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 frameshift, stop_lost

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.83

Variant links:

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]

SLC7A13 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

PM4

Stoplost variant in NM_138817.3

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.

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	Protein	UniProt
SLC7A13	NM_138817.3 linkuse as main transcript	c.1413_*7delGATGTCGG	p.Ter471fs	frameshift_variant, stop_lost	4/4	ENST00000297524.8	NP_620172.2	Q8TCU3-1
SLC7A13	NM_138817.3 linkuse as main transcript	c.1412_*7delGATGTCGG		3_prime_UTR_variant	4/4	ENST00000297524.8	NP_620172.2	Q8TCU3-1
SLC7A13	XM_011516867.3 linkuse as main transcript	c.1386_*7delGATGTCGG	p.Ter462fs	frameshift_variant, stop_lost	4/4		XP_011515169.1
SLC7A13	XM_011516867.3 linkuse as main transcript	c.1385_*7delGATGTCGG		3_prime_UTR_variant	4/4		XP_011515169.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
SLC7A13	ENST00000297524.8 linkuse as main transcript	c.1413_*7delGATGTCGG	p.Ter471fs	frameshift_variant, stop_lost	4/4	1	NM_138817.3	ENSP00000297524.3	Q8TCU3-1
SLC7A13	ENST00000297524 linkuse as main transcript	c.1412_*7delGATGTCGG		3_prime_UTR_variant	4/4	1	NM_138817.3	ENSP00000297524.3	Q8TCU3-1
SLC7A13	ENST00000419776.2 linkuse as main transcript	c.212_219delGATGTCGG		3_prime_UTR_variant	5/5	1		ENSP00000410982.2	Q8TCU3-2

Frequencies

GnomAD3 genomes

AF:

0.129

AC:

19557

AN:

151998

Hom.:

1700

Cov.:

show subpopulations

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

show subpopulations

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

show subpopulations

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.:

AF XY:

0.132

AC XY:

9837

AN XY:

74348

show subpopulations

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

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 30, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over