rs4149170

Positions:

• chr11-62984817-C-T

Variant summary

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

The NM_153276.3(SLC22A6):​c.-127G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 1,086,636 control chromosomes in the GnomAD database, including 8,846 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 0.17 (3094 hom., cov: 31)
  • Exomes 𝑓: 0.096 (5752 hom.)
• Consequence: SLC22A6 NM_153276.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.284

Genes affected

SLC22A6 (HGNC:10970): (solute carrier family 22 member 6) The protein encoded by this gene is involved in the sodium-dependent transport and excretion of organic anions, some of which are potentially toxic. The encoded protein is an integral membrane protein and may be localized to the basolateral membrane. Four transcript variants encoding four different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC22A6	NM_153276.3	c.-127G>A		5_prime_UTR_variant	1/10	ENST00000360421.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC22A6	ENST00000360421.9	c.-127G>A		5_prime_UTR_variant	1/10	1	NM_153276.3	P1
SLC22A6	ENST00000377871.7	c.-127G>A		5_prime_UTR_variant	1/10	1
SLC22A6	ENST00000540654.5	c.-127G>A		5_prime_UTR_variant, NMD_transcript_variant	1/10	5

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25377 AN: 151982 Hom.: 3067 Cov.: 31

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.0836

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0852

Gnomad OTH AF: 0.150

GnomAD4 exome AF: 0.0960 AC: 89723 AN: 934538 Hom.: 5752 Cov.: 13 AF XY: 0.0974 AC XY: 45415 AN XY: 466036

Gnomad4 AFR exome AF: 0.331

Gnomad4 AMR exome AF: 0.116

Gnomad4 ASJ exome AF: 0.0853

Gnomad4 EAS exome AF: 0.230

Gnomad4 SAS exome AF: 0.157

Gnomad4 FIN exome AF: 0.100

Gnomad4 NFE exome AF: 0.0762

Gnomad4 OTH exome AF: 0.110

GnomAD4 genome AF: 0.167 AC: 25452 AN: 152098 Hom.: 3094 Cov.: 31 AF XY: 0.167 AC XY: 12429 AN XY: 74368

Gnomad4 AFR AF: 0.335

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.0836

Gnomad4 EAS AF: 0.244

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.0852

Gnomad4 OTH AF: 0.155

Alfa AF: 0.105 Hom.: 1294

Bravo AF: 0.177

Asia WGS AF: 0.209 AC: 728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	17
DANN	Benign	0.86

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: rs4149170; hg19: chr11-62752289;