rs4975625

Variant names:

• chr5-1228100-G-A
• rs4975625
• NM_182632.3:c.160+2463G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-1228100-G-A
• chr5-1228100-G-C

Variant summary

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

The NM_182632.3(SLC6A18):​c.160+2463G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 151,858 control chromosomes in the GnomAD database, including 11,925 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 0.39 (11925 hom., cov: 33)
• Consequence: SLC6A18 NM_182632.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.14
• Publications: 5 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_182632.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC6A18	NM_182632.3	MANE Select	c.160+2463G>A		intron	N/A	NP_872438.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC6A18	ENST00000324642.4	TSL:1 MANE Select	c.160+2463G>A		intron	N/A	ENSP00000323549.3
	SLC6A18	ENST00000513607.2	TSL:3	n.229+2463G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59681 AN: 151740 Hom.: 11913 Cov.: 33

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.393 AC: 59729 AN: 151858 Hom.: 11925 Cov.: 33 AF XY: 0.391 AC XY: 29035 AN XY: 74202

African (AFR) AF: 0.349 AC: 14457 AN: 41412

American (AMR) AF: 0.423 AC: 6445 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1229 AN: 3468

East Asian (EAS) AF: 0.233 AC: 1206 AN: 5174

South Asian (SAS) AF: 0.349 AC: 1683 AN: 4820

European-Finnish (FIN) AF: 0.403 AC: 4238 AN: 10528

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.431 AC: 29239 AN: 67896

Other (OTH) AF: 0.388 AC: 818 AN: 2106

Alfa AF: 0.406 Hom.: 8987

Bravo AF: 0.392

Asia WGS AF: 0.305 AC: 1059 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.56
PhyloP100		-2.1
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: rs4975625; hg19: chr5-1228215;