chr1-53124958-T-C

Variant names:

• chr1-53124958-T-C
• rs3766793
• NM_006671.6:c.215+9392A>G

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+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
• Publications: 1 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=-0.85).
• 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 rank	MANE	Protein	UniProt
SLC1A7	NM_006671.6	c.215+9392A>G		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.215+9392A>G		intron_variant	Intron 2 of 10	1	NM_006671.6	ENSP00000360549.5

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

African (AFR) AF: 0.365 AC: 15141 AN: 41470

American (AMR) AF: 0.175 AC: 2681 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 460 AN: 3466

East Asian (EAS) AF: 0.316 AC: 1635 AN: 5166

South Asian (SAS) AF: 0.489 AC: 2359 AN: 4820

European-Finnish (FIN) AF: 0.177 AC: 1876 AN: 10582

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10795 AN: 68010

Other (OTH) AF: 0.210 AC: 444 AN: 2116

Alfa AF: 0.181 Hom.: 4988

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
PhyloP100		0.37
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: rs3766793; hg19: chr1-53590630;