rs4795541

Variant names:

• chr17-30237299-A-G
• rs4795541
• ENST00000855095.1:c.-124+1088T>C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000855095.1(SLC6A4):​c.-124+1088T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0011 (0 hom., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: SLC6A4 ENST00000855095.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.910
• Publications: 68 publications found

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]

SLC6A4 Gene-Disease associations (from GenCC):

• obsessive-compulsive disorder

  Inheritance: AD Classification: LIMITED Submitted by: PanelApp Australia
• autism spectrum disorder

  Inheritance: AD Classification: NO_KNOWN Submitted by: ClinGen

ENSG00000266120 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000855095.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC6A4	ENST00000855095.1		c.-124+1088T>C		intron	N/A	ENSP00000525154.1
	SLC6A4	ENST00000855096.1		c.-221+1088T>C		intron	N/A	ENSP00000525155.1
	ENSG00000266120	ENST00000724731.1		n.109+229A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00108 AC: 13 AN: 12010 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000733

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00134

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0109

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00216

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00118

Gnomad OTH AF: 0.00

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00108 AC: 13 AN: 12024 Hom.: 0 Cov.: 0 AF XY: 0.00110 AC XY: 6 AN XY: 5438

African (AFR) AF: 0.000731 AC: 3 AN: 4102

American (AMR) AF: 0.00134 AC: 1 AN: 748

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 262

East Asian (EAS) AF: 0.0111 AC: 1 AN: 90

South Asian (SAS) AF: 0.00 AC: 0 AN: 178

European-Finnish (FIN) AF: 0.00216 AC: 1 AN: 462

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 16

European-Non Finnish (NFE) AF: 0.00118 AC: 7 AN: 5954

Other (OTH) AF: 0.00 AC: 0 AN: 116

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	2.2
DANN	Benign	0.34
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs4795541; hg19: chr17-28564317;