Variant chr8-86217473-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_138817.3(SLC7A13):c.1176T>C(p.Tyr392Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 1,536,390 control chromosomes in the GnomAD database, including 19,769 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.14 ( 1921 hom., cov: 33)

Exomes 𝑓: 0.15 ( 17848 hom. )

Consequence

SLC7A13
NM_138817.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.48

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 -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.51).

BP6

Variant 8-86217473-A-G is Benign according to our data. Variant chr8-86217473-A-G is described in ClinVar as [Benign]. Clinvar id is 1545666.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=1.48 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.319 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.1176T>C	p.Tyr392Tyr	synonymous_variant	3/4	ENST00000297524.8	NP_620172.2	Q8TCU3-1
SLC7A13	XM_011516867.3 linkuse as main transcript	c.1149T>C	p.Tyr383Tyr	synonymous_variant	3/4		XP_011515169.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC7A13	ENST00000297524.8 linkuse as main transcript	c.1176T>C	p.Tyr392Tyr	synonymous_variant	3/4	1	NM_138817.3	ENSP00000297524.3		Q8TCU3-1
SLC7A13	ENST00000419776.2 linkuse as main transcript	c.1149T>C	p.Tyr383Tyr	synonymous_variant	3/5	1		ENSP00000410982.2		Q8TCU3-2

Frequencies

GnomAD3 genomes

AF:

0.141

AC:

21430

AN:

152000

Hom.:

1915

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0919

Gnomad AMI

AF:

0.141

Gnomad AMR

AF:

0.185

Gnomad ASJ

AF:

0.200

Gnomad EAS

AF:

0.331

Gnomad SAS

AF:

0.321

Gnomad FIN

AF:

0.114

Gnomad MID

AF:

0.245

Gnomad NFE

AF:

0.134

Gnomad OTH

AF:

0.158

GnomAD3 exomes

AF:

0.179

AC:

34495

AN:

193064

Hom.:

3823

AF XY:

0.182

AC XY:

19034

AN XY:

104440

show subpopulations

Gnomad AFR exome

AF:

0.0918

Gnomad AMR exome

AF:

0.239

Gnomad ASJ exome

AF:

0.199

Gnomad EAS exome

AF:

0.329

Gnomad SAS exome

AF:

0.318

Gnomad FIN exome

AF:

0.117

Gnomad NFE exome

AF:

0.137

Gnomad OTH exome

AF:

0.172

GnomAD4 exome

AF:

0.146

AC:

202533

AN:

1384272

Hom.:

17848

Cov.:

AF XY:

0.152

AC XY:

103972

AN XY:

685076

show subpopulations

Gnomad4 AFR exome

AF:

0.0888

Gnomad4 AMR exome

AF:

0.228

Gnomad4 ASJ exome

AF:

0.196

Gnomad4 EAS exome

AF:

0.323

Gnomad4 SAS exome

AF:

0.318

Gnomad4 FIN exome

AF:

0.118

Gnomad4 NFE exome

AF:

0.127

Gnomad4 OTH exome

AF:

0.160

GnomAD4 genome

AF:

0.141

AC:

21460

AN:

152118

Hom.:

1921

Cov.:

AF XY:

0.145

AC XY:

10770

AN XY:

74364

show subpopulations

Gnomad4 AFR

AF:

0.0919

Gnomad4 AMR

AF:

0.185

Gnomad4 ASJ

AF:

0.200

Gnomad4 EAS

AF:

0.332

Gnomad4 SAS

AF:

0.322

Gnomad4 FIN

AF:

0.114

Gnomad4 NFE

AF:

0.134

Gnomad4 OTH

AF:

0.161

Alfa

AF:

0.138

Hom.:

999

Bravo

AF:

0.142

Asia WGS

AF:

0.342

AC:

1187

AN:

3472

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

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	Labcorp Genetics (formerly Invitae), Labcorp	Jan 30, 2024	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.51

CADD

Benign

2.0

DANN

Benign

0.49

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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

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