Genetic Variant NM_032803.6:c.1522C>T (chrX-70926625-G-A) – ACMG Classification: Likely_benign (-3 pts)

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7

The NM_032803.6(SLC7A3):c.1522C>T(p.Leu508Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 22)

Exomes 𝑓: 0.0 ( 0 hom. 0 hem. )

Failed GnomAD Quality Control

Consequence

SLC7A3
NM_032803.6 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.420

Publications

22 publications found

Variant links:

Genes affected

SLC7A3 (HGNC:11061): (solute carrier family 7 member 3) This gene encodes a member of the solute carrier family 7. The encoded protein is a sodium-independent cationic amino acid transporter. Alternate splicing results in multiple transcripts that encoded the same protein.[provided by RefSeq, May 2010]

SLC7A3 Gene-Disease associations (from GenCC):

autism spectrum disorder
Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

SLC7A3 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -3 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.68).

BP7

Synonymous conserved (PhyloP=-0.42 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein
SLC7A3	NM_032803.6 link	c.1522C>T	p.Leu508Leu	synonymous_variant	Exon 10 of 12	ENST00000374299.8	NP_116192.4
SLC7A3	NM_001048164.3 link	c.1522C>T	p.Leu508Leu	synonymous_variant	Exon 10 of 12		NP_001041629.1
SLC7A3	XM_047442598.1 link	c.1522C>T	p.Leu508Leu	synonymous_variant	Exon 9 of 11		XP_047298554.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC7A3	ENST00000374299.8 link	c.1522C>T	p.Leu508Leu	synonymous_variant	Exon 10 of 12	1	NM_032803.6	ENSP00000363417.3
SLC7A3	ENST00000298085.4 link	c.1522C>T	p.Leu508Leu	synonymous_variant	Exon 10 of 12	2		ENSP00000298085.4

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1081653

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

352285

African (AFR)

AF:

0.00

AC:

AN:

26088

American (AMR)

AF:

0.00

AC:

AN:

32497

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

19051

East Asian (EAS)

AF:

0.00

AC:

AN:

29660

South Asian (SAS)

AF:

0.00

AC:

AN:

51631

European-Finnish (FIN)

AF:

0.00

AC:

AN:

39576

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3929

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

833658

Other (OTH)

AF:

0.00

AC:

AN:

45563

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

1.8

(source)

DANN

Benign

0.49

PhyloP100

-0.42

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over