11-62984186-G-A

Variant names:

• chr11-62984186-G-A
• rs10897312
• NM_153276.3:c.369+136C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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]

ENSG00000301851 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_153276.3. 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
	SLC22A6	NM_153276.3	MANE Select	c.369+136C>T		intron	N/A	NP_695008.1
	SLC22A6	NM_004790.5		c.369+136C>T		intron	N/A	NP_004781.2
	SLC22A6	NM_153278.3		c.369+136C>T		intron	N/A	NP_695010.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC22A6	ENST00000360421.9	TSL:1 MANE Select	c.369+136C>T		intron	N/A	ENSP00000353597.4
	SLC22A6	ENST00000377871.7	TSL:1	c.369+136C>T		intron	N/A	ENSP00000367102.3
	SLC22A6	ENST00000421062.2	TSL:1	c.369+136C>T		intron	N/A	ENSP00000404441.2

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

African (AFR) AF: 0.348 AC: 8645 AN: 24816

American (AMR) AF: 0.121 AC: 2891 AN: 23848

Ashkenazi Jewish (ASJ) AF: 0.0870 AC: 1657 AN: 19052

East Asian (EAS) AF: 0.232 AC: 8020 AN: 34550

South Asian (SAS) AF: 0.163 AC: 10137 AN: 62198

European-Finnish (FIN) AF: 0.101 AC: 4706 AN: 46594

Middle Eastern (MID) AF: 0.183 AC: 892 AN: 4876

European-Non Finnish (NFE) AF: 0.0807 AC: 69686 AN: 863904

Other (OTH) AF: 0.116 AC: 5626 AN: 48356

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

African (AFR) AF: 0.335 AC: 13862 AN: 41388

American (AMR) AF: 0.118 AC: 1795 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0840 AC: 291 AN: 3466

East Asian (EAS) AF: 0.244 AC: 1250 AN: 5118

South Asian (SAS) AF: 0.175 AC: 842 AN: 4804

European-Finnish (FIN) AF: 0.108 AC: 1133 AN: 10470

Middle Eastern (MID) AF: 0.141 AC: 41 AN: 290

European-Non Finnish (NFE) AF: 0.0853 AC: 5801 AN: 67968

Other (OTH) AF: 0.156 AC: 328 AN: 2106

Alfa AF: 0.112 Hom.: 2530

Bravo AF: 0.177

Asia WGS AF: 0.213 AC: 741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.7
DANN	Benign	0.54
PhyloP100		0.034
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10897312; hg19: chr11-62751658;