1-53088042-G-A

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_Strong BP6_Moderate BP7 BS2

The NM_006671.6(SLC1A7):c.1650C>T(p.Thr550=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00366 in 1,564,566 control chromosomes in the GnomAD database, including 65 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0058 (15 hom., cov: 33)
  • Exomes 𝑓: 0.0034 (50 hom.)
• Consequence: SLC1A7 NM_006671.6 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.655

Genes affected

SLC1A7 (HGNC:10945): (solute carrier family 1 member 7) Predicted to enable anion transmembrane transporter activity. Involved in neurotransmitter reuptake. Predicted to be located in plasma membrane. Predicted to be active in glutamatergic synapse. Predicted to be integral component of postsynaptic membrane and integral component of presynaptic membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -11 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BP6: Variant 1-53088042-G-A is Benign according to our data. Variant chr1-53088042-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2638821.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=0.655 with no splicing effect.
• BS2: High Homozygotes in GnomAd at 15 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC1A7	NM_006671.6	c.1650C>T	p.Thr550=	synonymous_variant	11/11	ENST00000371494.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC1A7	ENST00000371494.9	c.1650C>T	p.Thr550=	synonymous_variant	11/11	1	NM_006671.6	P1

Frequencies

GnomAD3 genomes AF: 0.00583 AC: 887 AN: 152174 Hom.: 15 Cov.: 33

Gnomad AFR AF: 0.000169

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000720

Gnomad ASJ AF: 0.00749

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.0398

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00609

Gnomad OTH AF: 0.00287

GnomAD3 exomes AF: 0.00632 AC: 1452 AN: 229744 Hom.: 17 AF XY: 0.00601 AC XY: 743 AN XY: 123656

Gnomad AFR exome AF: 0.000316

Gnomad AMR exome AF: 0.000386

Gnomad ASJ exome AF: 0.00545

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.0389

Gnomad NFE exome AF: 0.00515

Gnomad OTH exome AF: 0.00748

GnomAD4 exome AF: 0.00343 AC: 4843 AN: 1412274 Hom.: 50 Cov.: 40 AF XY: 0.00342 AC XY: 2381 AN XY: 696428

Gnomad4 AFR exome AF: 0.000184

Gnomad4 AMR exome AF: 0.000361

Gnomad4 ASJ exome AF: 0.00624

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0385

Gnomad4 NFE exome AF: 0.00226

Gnomad4 OTH exome AF: 0.00358

GnomAD4 genome AF: 0.00582 AC: 886 AN: 152292 Hom.: 15 Cov.: 33 AF XY: 0.00755 AC XY: 562 AN XY: 74456

Gnomad4 AFR AF: 0.000168

Gnomad4 AMR AF: 0.000654

Gnomad4 ASJ AF: 0.00749

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.0398

Gnomad4 NFE AF: 0.00609

Gnomad4 OTH AF: 0.00284

Alfa AF: 0.00568 Hom.: 5

Bravo AF: 0.00186

Asia WGS AF: 0.000577 AC: 2 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Feb 01, 2023

SLC1A7: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
Cadd	Benign	6.9
Dann	Benign	0.64

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

Publications

LitVar

Other links and lift over

dbSNP: rs140010762; hg19: chr1-53553714;