rs899976

Variant names:

• chr1-53128141-G-A
• rs899976
• NM_006671.6:c.215+6209C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006671.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC1A7	NM_006671.6	MANE Select	c.215+6209C>T		intron	N/A	NP_006662.3
	SLC1A7	NM_001287595.2		c.215+6209C>T		intron	N/A	NP_001274524.1
	SLC1A7	NM_001287597.2		c.215+6209C>T		intron	N/A	NP_001274526.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC1A7	ENST00000371494.9	TSL:1 MANE Select	c.215+6209C>T		intron	N/A	ENSP00000360549.5
	SLC1A7	ENST00000620347.5	TSL:1	c.215+6209C>T		intron	N/A	ENSP00000478639.1
	SLC1A7	ENST00000611397.5	TSL:1	c.215+6209C>T		intron	N/A	ENSP00000484987.1

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

African (AFR) AF: 0.399 AC: 16555 AN: 41448

American (AMR) AF: 0.270 AC: 4124 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 1085 AN: 3472

East Asian (EAS) AF: 0.294 AC: 1519 AN: 5160

South Asian (SAS) AF: 0.208 AC: 1000 AN: 4812

European-Finnish (FIN) AF: 0.200 AC: 2117 AN: 10586

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.233 AC: 15829 AN: 67996

Other (OTH) AF: 0.288 AC: 607 AN: 2110

Alfa AF: 0.268 Hom.: 1076

Bravo AF: 0.297

Asia WGS AF: 0.245 AC: 853 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.72
PhyloP100		1.2
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: rs899976; hg19: chr1-53593813;