rs3766793

Positions:

• chr1-53124958-T-C
• chr1-53124958-T-G

Variant summary

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

The NM_006671.6(SLC1A7):​c.215+9392A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 152,134 control chromosomes in the GnomAD database, including 4,939 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 0.23 (4939 hom., cov: 33)
• Consequence: SLC1A7 NM_006671.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.371

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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC1A7	NM_006671.6	c.215+9392A>G		intron_variant		ENST00000371494.9	NP_006662.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC1A7	ENST00000371494.9	c.215+9392A>G		intron_variant		1	NM_006671.6	ENSP00000360549	P1

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35523 AN: 152016 Hom.: 4937 Cov.: 33

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.234 AC: 35535 AN: 152134 Hom.: 4939 Cov.: 33 AF XY: 0.238 AC XY: 17724 AN XY: 74354

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.316

Gnomad4 SAS AF: 0.489

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.210

Alfa AF: 0.177 Hom.: 3766

Bravo AF: 0.229

Asia WGS AF: 0.413 AC: 1436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.3
DANN	Benign	0.70

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: rs3766793; hg19: chr1-53590630;