rs17306977

chr16-55659461-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001172501.3(SLC6A2):c.274+2493A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,142 control chromosomes in the GnomAD database, including 896 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 0.10 (896 hom., cov: 32)
• Consequence: SLC6A2 NM_001172501.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC6A2	NM_001172501.3	c.274+2493A>T		intron_variant		ENST00000568943.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC6A2	ENST00000568943.6	c.274+2493A>T		intron_variant		1	NM_001172501.3	P1

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15592 AN: 152024 Hom.: 897 Cov.: 32

Gnomad AFR AF: 0.0787

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.0949

Gnomad ASJ AF: 0.0877

Gnomad EAS AF: 0.0147

Gnomad SAS AF: 0.0718

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.0970

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

GnomAD4 genome AF: 0.103 AC: 15605 AN: 152142 Hom.: 896 Cov.: 32 AF XY: 0.105 AC XY: 7782 AN XY: 74378

Gnomad4 AFR AF: 0.0787

Gnomad4 AMR AF: 0.0947

Gnomad4 ASJ AF: 0.0877

Gnomad4 EAS AF: 0.0145

Gnomad4 SAS AF: 0.0720

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.0989

Alfa AF: 0.111 Hom.: 127

Bravo AF: 0.0915

Asia WGS AF: 0.0700 AC: 243 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	5.0
Dann	Benign	0.48

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

Publications

LitVar

Other links and lift over

dbSNP: rs17306977; hg19: chr16-55693373;