chr1-53140408-C-T

Variant names:

• chr1-53140408-C-T
• rs11206109
• NM_006671.6:c.135+1907G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006671.6(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 NM_006671.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146
• Publications: 15 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.354 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.135+1907G>A		intron	N/A	NP_006662.3
	SLC1A7	NM_001287595.2		c.135+1907G>A		intron	N/A	NP_001274524.1
	SLC1A7	NM_001287597.2		c.135+1907G>A		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.135+1907G>A		intron	N/A	ENSP00000360549.5
	SLC1A7	ENST00000620347.5	TSL:1	c.135+1907G>A		intron	N/A	ENSP00000478639.1
	SLC1A7	ENST00000611397.5	TSL:1	c.135+1907G>A		intron	N/A	ENSP00000484987.1

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

African (AFR) AF: 0.231 AC: 9567 AN: 41396

American (AMR) AF: 0.362 AC: 5534 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 887 AN: 3470

East Asian (EAS) AF: 0.309 AC: 1593 AN: 5154

South Asian (SAS) AF: 0.159 AC: 765 AN: 4814

European-Finnish (FIN) AF: 0.245 AC: 2564 AN: 10478

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.272 AC: 18447 AN: 67928

Other (OTH) AF: 0.289 AC: 609 AN: 2108

Alfa AF: 0.269 Hom.: 21132

Bravo AF: 0.276

Asia WGS AF: 0.231 AC: 802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.2
DANN	Benign	0.71
PhyloP100		0.15
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: rs11206109; hg19: chr1-53606080;