chr12-223196-C-T

Variant names:

• chr12-223196-C-T
• rs2289954
• NM_016615.5:c.1350G>A

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_016615.5(SLC6A13):​c.1350G>A​(p.Ala450Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 1,611,478 control chromosomes in the GnomAD database, including 31,412 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 0.20 (3120 hom., cov: 32)
  • Exomes 𝑓: 0.19 (28292 hom.)
• Consequence: SLC6A13 NM_016615.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90
• Publications: 22 publications found

Genes affected

SLC6A13 (HGNC:11046): (solute carrier family 6 member 13) Enables amino acid transmembrane transporter activity and monocarboxylic acid transmembrane transporter activity. Involved in amino acid import across plasma membrane and monocarboxylic acid transport. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BP7: Synonymous conserved (PhyloP=-1.9 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.227 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC6A13	NM_016615.5	c.1350G>A	p.Ala450Ala	synonymous_variant	Exon 12 of 15	ENST00000343164.9	NP_057699.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC6A13	ENST00000343164.9	c.1350G>A	p.Ala450Ala	synonymous_variant	Exon 12 of 15	1	NM_016615.5	ENSP00000339260.4
SLC6A13	ENST00000445055.6	c.1074G>A	p.Ala358Ala	synonymous_variant	Exon 10 of 13	2		ENSP00000407104.2
SLC6A13	ENST00000539668.1	n.308G>A		non_coding_transcript_exon_variant	Exon 4 of 5	5
SLC6A13	ENST00000542379.1	n.258G>A		non_coding_transcript_exon_variant	Exon 3 of 3	3

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30372 AN: 151896 Hom.: 3115 Cov.: 32

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.194

GnomAD2 exomes AF: 0.185 AC: 46512 AN: 251030 AF XY: 0.188

Gnomad AFR exome AF: 0.231

Gnomad AMR exome AF: 0.108

Gnomad ASJ exome AF: 0.223

Gnomad EAS exome AF: 0.170

Gnomad FIN exome AF: 0.201

Gnomad NFE exome AF: 0.199

Gnomad OTH exome AF: 0.190

GnomAD4 exome AF: 0.193 AC: 282057 AN: 1459466 Hom.: 28292 Cov.: 31 AF XY: 0.193 AC XY: 140195 AN XY: 726170

African (AFR) AF: 0.235 AC: 7865 AN: 33398

American (AMR) AF: 0.113 AC: 5056 AN: 44666

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 5933 AN: 26104

East Asian (EAS) AF: 0.159 AC: 6306 AN: 39670

South Asian (SAS) AF: 0.178 AC: 15361 AN: 86170

European-Finnish (FIN) AF: 0.201 AC: 10718 AN: 53378

Middle Eastern (MID) AF: 0.224 AC: 1292 AN: 5762

European-Non Finnish (NFE) AF: 0.197 AC: 218166 AN: 1109990

Other (OTH) AF: 0.188 AC: 11360 AN: 60328

GnomAD4 genome AF: 0.200 AC: 30405 AN: 152012 Hom.: 3120 Cov.: 32 AF XY: 0.199 AC XY: 14809 AN XY: 74290

African (AFR) AF: 0.231 AC: 9552 AN: 41436

American (AMR) AF: 0.149 AC: 2286 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 818 AN: 3466

East Asian (EAS) AF: 0.160 AC: 825 AN: 5162

South Asian (SAS) AF: 0.174 AC: 836 AN: 4808

European-Finnish (FIN) AF: 0.203 AC: 2147 AN: 10580

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.195 AC: 13228 AN: 67944

Other (OTH) AF: 0.193 AC: 409 AN: 2116

Alfa AF: 0.191 Hom.: 5372

Bravo AF: 0.200

Asia WGS AF: 0.153 AC: 531 AN: 3478

EpiCase AF: 0.192

EpiControl AF: 0.191

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	0.49
DANN	Benign	0.69
PhyloP100		-1.9
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: rs2289954; hg19: chr12-332362; COSMIC: COSV58255963; COSMIC: COSV58255963;