Variant rs1610905 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000568943.6(SLC6A2):c.274+950_274+951insGGTGCCCAGTCCTGC variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.49 ( 18729 hom., cov: 0)

Consequence

SLC6A2
ENST00000568943.6 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0720

Variant links:

Genes affected

SLC6A2 (HGNC:11048): (solute carrier family 6 member 2) This gene encodes a member of the sodium:neurotransmitter symporter family. This member is a multi-pass membrane protein, which is responsible for reuptake of norepinephrine into presynaptic nerve terminals and is a regulator of norepinephrine homeostasis. Mutations in this gene cause orthostatic intolerance, a syndrome characterized by lightheadedness, fatigue, altered mentation and syncope. Alternatively spliced transcript variants encoding different isoforms have been identified in this gene.[provided by RefSeq, Feb 2010]

SLC6A2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC6A2	NM_001172501.3 linkuse as main transcript	c.274+950_274+951insGGTGCCCAGTCCTGC		intron_variant		ENST00000568943.6	NP_001165972.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC6A2	ENST00000568943.6 linkuse as main transcript	c.274+950_274+951insGGTGCCCAGTCCTGC		intron_variant		1	NM_001172501.3	ENSP00000457473	P1	P23975-1

Frequencies

GnomAD3 genomes

AF:

0.492

AC:

74705

AN:

151704

Hom.:

18722

Cov.:

show subpopulations

Gnomad AFR

AF:

0.395

Gnomad AMI

AF:

0.576

Gnomad AMR

AF:

0.539

Gnomad ASJ

AF:

0.484

Gnomad EAS

AF:

0.463

Gnomad SAS

AF:

0.535

Gnomad FIN

AF:

0.589

Gnomad MID

AF:

0.379

Gnomad NFE

AF:

0.524

Gnomad OTH

AF:

0.507

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.492

AC:

74747

AN:

151822

Hom.:

18729

Cov.:

AF XY:

0.499

AC XY:

37041

AN XY:

74174

show subpopulations

Gnomad4 AFR

AF:

0.395

Gnomad4 AMR

AF:

0.539

Gnomad4 ASJ

AF:

0.484

Gnomad4 EAS

AF:

0.462

Gnomad4 SAS

AF:

0.536

Gnomad4 FIN

AF:

0.589

Gnomad4 NFE

AF:

0.524

Gnomad4 OTH

AF:

0.509

Alfa

AF:

0.328

Hom.:

665

Asia WGS

AF:

0.474

AC:

1646

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over