X-70927830-C-T

Variant names:

• chrX-70927830-C-T
• rs1602237099
• NM_032803.6:c.1011G>A

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2 BP4_Moderate BP7

The NM_032803.6(SLC7A3):​c.1011G>A​(p.Val337Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000093 in 1,074,699 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. V337V) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 23)
  • Exomes 𝑓: 9.3e-7 (0 hom. 0 hem.)
• Consequence: SLC7A3 NM_032803.6 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01
• Publications: 0 publications found

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

ENSG00000295939 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BP7: Synonymous conserved (PhyloP=1.01 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032803.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC7A3	NM_032803.6	MANE Select	c.1011G>A	p.Val337Val	synonymous	Exon 6 of 12	NP_116192.4
	SLC7A3	NM_001048164.3		c.1011G>A	p.Val337Val	synonymous	Exon 6 of 12	NP_001041629.1	Q8WY07

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC7A3	ENST00000374299.8	TSL:1 MANE Select	c.1011G>A	p.Val337Val	synonymous	Exon 6 of 12	ENSP00000363417.3	Q8WY07
	SLC7A3	ENST00000921007.1		c.1011G>A	p.Val337Val	synonymous	Exon 6 of 13	ENSP00000591066.1
	SLC7A3	ENST00000921008.1		c.1011G>A	p.Val337Val	synonymous	Exon 6 of 13	ENSP00000591067.1

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome AF: 9.30e-7 AC: 1 AN: 1074699 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 350237

African (AFR) AF: 0.00 AC: 0 AN: 25896

American (AMR) AF: 0.00 AC: 0 AN: 30778

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18874

East Asian (EAS) AF: 0.00 AC: 0 AN: 29006

South Asian (SAS) AF: 0.00 AC: 0 AN: 51203

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 39124

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4111

European-Non Finnish (NFE) AF: 0.00000120 AC: 1 AN: 830360

Other (OTH) AF: 0.00 AC: 0 AN: 45347

GnomAD4 genome Cov.: 23

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	8.1
DANN	Benign	0.70
PhyloP100		1.0

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

Other links and lift over

dbSNP: rs1602237099; hg19: chrX-70147680;