chr16-55679176-C-T

Position:

• chr16-55679176-C-T

Variant summary

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

The NM_001172501.3(SLC6A2):​c.645-5967C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 151,980 control chromosomes in the GnomAD database, including 1,082 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 0.11 (1082 hom., cov: 32)
• Consequence: SLC6A2 NM_001172501.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.28

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC6A2	NM_001172501.3	c.645-5967C>T		intron_variant		ENST00000568943.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC6A2	ENST00000568943.6	c.645-5967C>T		intron_variant		1	NM_001172501.3	P1

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17241 AN: 151886 Hom.: 1078 Cov.: 32

Gnomad AFR AF: 0.0590

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.0788

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.173

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.114 AC: 17255 AN: 151980 Hom.: 1082 Cov.: 32 AF XY: 0.114 AC XY: 8432 AN XY: 74252

Gnomad4 AFR AF: 0.0589

Gnomad4 AMR AF: 0.101

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.168

Gnomad4 SAS AF: 0.0794

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.124

Alfa AF: 0.130 Hom.: 1334

Bravo AF: 0.107

Asia WGS AF: 0.130 AC: 452 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.075
DANN	Benign	0.21

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: rs36020; hg19: chr16-55713088;