rs899976

chr1-53128141-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006671.6(SLC1A7):c.215+6209C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 152,072 control chromosomes in the GnomAD database, including 6,638 homozygotes. 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: 𝑓 0.28 (6638 hom., cov: 33)
• Consequence: SLC1A7 NM_006671.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC1A7	NM_006671.6	c.215+6209C>T		intron_variant		ENST00000371494.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC1A7	ENST00000371494.9	c.215+6209C>T		intron_variant		1	NM_006671.6	P1

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43276 AN: 151956 Hom.: 6625 Cov.: 33

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.289

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.285 AC: 43326 AN: 152072 Hom.: 6638 Cov.: 33 AF XY: 0.281 AC XY: 20862 AN XY: 74320

Gnomad4 AFR AF: 0.399

Gnomad4 AMR AF: 0.270

Gnomad4 ASJ AF: 0.313

Gnomad4 EAS AF: 0.294

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.200

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.288

Alfa AF: 0.265 Hom.: 1026

Bravo AF: 0.297

Asia WGS AF: 0.245 AC: 853 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.4
Dann	Benign	0.72

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: rs899976; hg19: chr1-53593813;