rs11206109

Positions:

• chr1-53140408-C-T

Variant summary

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

The ENST00000371494.9(SLC1A7):​c.135+1907G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 151,820 control chromosomes in the GnomAD database, including 5,550 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 0.27 (5550 hom., cov: 33)
• Consequence: SLC1A7 ENST00000371494.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146

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=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC1A7	NM_006671.6	c.135+1907G>A		intron_variant		ENST00000371494.9	NP_006662.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC1A7	ENST00000371494.9	c.135+1907G>A		intron_variant		1	NM_006671.6	ENSP00000360549	P1

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40252 AN: 151704 Hom.: 5543 Cov.: 33

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.265 AC: 40279 AN: 151820 Hom.: 5550 Cov.: 33 AF XY: 0.266 AC XY: 19701 AN XY: 74164

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.362

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.309

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.289

Alfa AF: 0.270 Hom.: 9346

Bravo AF: 0.276

Asia WGS AF: 0.231 AC: 802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.2
DANN	Benign	0.71

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: rs11206109; hg19: chr1-53606080;