5-1229052-C-T

Variant names:

• chr5-1229052-C-T
• rs12522796
• NM_182632.3:c.161-3167C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_182632.3(SLC6A18):​c.161-3167C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 152,194 control chromosomes in the GnomAD database, including 5,180 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 0.23 (5180 hom., cov: 33)
• Consequence: SLC6A18 NM_182632.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.663
• Publications: 1 publications found

Genes affected

SLC6A18 (HGNC:26441): (solute carrier family 6 member 18) The SLC6 family of proteins, which includes SLC6A18, act as specific transporters for neurotransmitters, amino acids, and osmolytes like betaine, taurine, and creatine. SLC6 proteins are sodium cotransporters that derive the energy for solute transport from the electrochemical gradient for sodium ions (Hoglund et al., 2005 [PubMed 16125675]).[supplied by OMIM, Apr 2010]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC6A18	NM_182632.3	c.161-3167C>T		intron_variant	Intron 1 of 11	ENST00000324642.4	NP_872438.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC6A18	ENST00000324642.4	c.161-3167C>T		intron_variant	Intron 1 of 11	1	NM_182632.3	ENSP00000323549.3
SLC6A18	ENST00000513607.2	n.230-3167C>T		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34891 AN: 152076 Hom.: 5180 Cov.: 33

Gnomad AFR AF: 0.0601

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.0673

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.229 AC: 34892 AN: 152194 Hom.: 5180 Cov.: 33 AF XY: 0.228 AC XY: 16950 AN XY: 74402

African (AFR) AF: 0.0600 AC: 2493 AN: 41564

American (AMR) AF: 0.201 AC: 3067 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 747 AN: 3466

East Asian (EAS) AF: 0.0670 AC: 347 AN: 5176

South Asian (SAS) AF: 0.196 AC: 945 AN: 4826

European-Finnish (FIN) AF: 0.338 AC: 3575 AN: 10592

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.338 AC: 22949 AN: 67958

Other (OTH) AF: 0.212 AC: 448 AN: 2110

Alfa AF: 0.245 Hom.: 2301

Bravo AF: 0.211

Asia WGS AF: 0.122 AC: 426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.6
DANN	Benign	0.52
PhyloP100		0.66
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12522796; hg19: chr5-1229167;