1-53115998-A-G

Position:

• chr1-53115998-A-G

Variant summary

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

The NM_006671.6(SLC1A7):​c.216-1025T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.527 in 152,108 control chromosomes in the GnomAD database, including 23,521 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 0.53 (23520 hom., cov: 33)
  • Exomes 𝑓: 0.50 (1 hom.)
• Consequence: SLC1A7 NM_006671.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.692

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC1A7	NM_006671.6	c.216-1025T>C		intron_variant		ENST00000371494.9
LOC105379783	XR_007066089.1	n.355-113A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC1A7	ENST00000371494.9	c.216-1025T>C		intron_variant		1	NM_006671.6	P1
	ENST00000439621.1	n.1423A>G		non_coding_transcript_exon_variant	1/2	2

Frequencies

GnomAD3 genomes AF: 0.526 AC: 80018 AN: 151982 Hom.: 23488 Cov.: 33

Gnomad AFR AF: 0.748

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.877

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.499

GnomAD4 exome AF: 0.500 AC: 4 AN: 8 Hom.: 1 Cov.: 0 AF XY: 0.750 AC XY: 3 AN XY: 4

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.527 AC: 80099 AN: 152100 Hom.: 23520 Cov.: 33 AF XY: 0.532 AC XY: 39551 AN XY: 74352

Gnomad4 AFR AF: 0.748

Gnomad4 AMR AF: 0.584

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.877

Gnomad4 SAS AF: 0.618

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.376

Gnomad4 OTH AF: 0.504

Alfa AF: 0.395 Hom.: 15596

Bravo AF: 0.548

Asia WGS AF: 0.755 AC: 2623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	11
DANN	Benign	0.83

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: rs3820201; hg19: chr1-53581670;