17-30224840-C-T

Variant summary

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

The NM_001045.6(SLC6A4):c.-220-1925G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0666 in 152,098 control chromosomes in the GnomAD database, including 466 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 0.067 (466 hom., cov: 31)
• Consequence: SLC6A4 NM_001045.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.636

Genes affected

SLC6A4 (HGNC:11050): (solute carrier family 6 member 4) This gene encodes an integral membrane protein that transports the neurotransmitter serotonin from synaptic spaces into presynaptic neurons. The encoded protein terminates the action of serotonin and recycles it in a sodium-dependent manner. This protein is a target of psychomotor stimulants, such as amphetamines and cocaine, and is a member of the sodium:neurotransmitter symporter family. A repeat length polymorphism in the promoter of this gene has been shown to affect the rate of serotonin uptake. There have been conflicting results in the literature about the possible effect, if any, that this polymorphism may play in behavior and depression. [provided by RefSeq, May 2019]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC6A4	NM_001045.6	c.-220-1925G>A		intron_variant		ENST00000650711.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC6A4	ENST00000650711.1	c.-220-1925G>A		intron_variant			NM_001045.6	P1
SLC6A4	ENST00000261707.7	c.-220-1925G>A		intron_variant		1		P1
SLC6A4	ENST00000394821.2	c.-220-1925G>A		intron_variant		1
SLC6A4	ENST00000401766.6	c.-123-2759G>A		intron_variant		5		P1

Frequencies

GnomAD3 genomes AF: 0.0667 AC: 10135 AN: 151980 Hom.: 466 Cov.: 31

Gnomad AFR AF: 0.0160

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.0633

Gnomad ASJ AF: 0.0836

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.00849

Gnomad FIN AF: 0.0750

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.0700

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

GnomAD4 genome AF: 0.0666 AC: 10135 AN: 152098 Hom.: 466 Cov.: 31 AF XY: 0.0646 AC XY: 4800 AN XY: 74354

Gnomad4 AFR AF: 0.0160

Gnomad4 AMR AF: 0.0633

Gnomad4 ASJ AF: 0.0836

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.00829

Gnomad4 FIN AF: 0.0750

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.0693

Alfa AF: 0.0909 Hom.: 372

Bravo AF: 0.0630

Asia WGS AF: 0.0120 AC: 44 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.30
Dann	Benign	0.57

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: rs4251417; hg19: chr17-28551858;