1-53115998-A-G

Variant names:

• chr1-53115998-A-G
• rs3820201
• NM_006671.6:c.216-1025T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 publications found

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]

ENSG00000235563 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SLC1A7	NM_006671.6	c.216-1025T>C		intron_variant	Intron 2 of 10	ENST00000371494.9	NP_006662.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC1A7	ENST00000371494.9	c.216-1025T>C		intron_variant	Intron 2 of 10	1	NM_006671.6	ENSP00000360549.5

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 3 AN: 6

Other (OTH) AF: 0.500 AC: 1 AN: 2

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

African (AFR) AF: 0.748 AC: 31027 AN: 41490

American (AMR) AF: 0.584 AC: 8930 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1158 AN: 3466

East Asian (EAS) AF: 0.877 AC: 4530 AN: 5168

South Asian (SAS) AF: 0.618 AC: 2979 AN: 4824

European-Finnish (FIN) AF: 0.415 AC: 4390 AN: 10576

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.376 AC: 25557 AN: 67962

Other (OTH) AF: 0.504 AC: 1067 AN: 2116

Alfa AF: 0.429 Hom.: 32239

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
PhyloP100		0.69
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3820201; hg19: chr1-53581670;