chr11-62984186-G-A

Position:

• chr11-62984186-G-A

Variant summary

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

The NM_153276.3(SLC22A6):​c.369+136C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 1,279,986 control chromosomes in the GnomAD database, including 10,387 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 (3086 hom., cov: 31)
  • Exomes 𝑓: 0.10 (7301 hom.)
• Consequence: SLC22A6 NM_153276.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0340

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=-0.79).
• 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	Protein	UniProt
SLC22A6	NM_153276.3	c.369+136C>T		intron_variant		ENST00000360421.9	NP_695008.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC22A6	ENST00000360421.9	c.369+136C>T		intron_variant		1	NM_153276.3	ENSP00000353597	P1

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25361 AN: 151696 Hom.: 3059 Cov.: 31

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.0840

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.147

Gnomad NFE AF: 0.0853

Gnomad OTH AF: 0.151

GnomAD4 exome AF: 0.0995 AC: 112260 AN: 1128194 Hom.: 7301 Cov.: 16 AF XY: 0.101 AC XY: 56517 AN XY: 560234

Gnomad4 AFR exome AF: 0.348

Gnomad4 AMR exome AF: 0.121

Gnomad4 ASJ exome AF: 0.0870

Gnomad4 EAS exome AF: 0.232

Gnomad4 SAS exome AF: 0.163

Gnomad4 FIN exome AF: 0.101

Gnomad4 NFE exome AF: 0.0807

Gnomad4 OTH exome AF: 0.116

GnomAD4 genome AF: 0.168 AC: 25436 AN: 151792 Hom.: 3086 Cov.: 31 AF XY: 0.167 AC XY: 12417 AN XY: 74136

Gnomad4 AFR AF: 0.335

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.0840

Gnomad4 EAS AF: 0.244

Gnomad4 SAS AF: 0.175

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.0853

Gnomad4 OTH AF: 0.156

Alfa AF: 0.102 Hom.: 1457

Bravo AF: 0.177

Asia WGS AF: 0.213 AC: 741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.7
DANN	Benign	0.54

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs10897312; hg19: chr11-62751658;