rs6591722

Positions:

• chr11-62982208-T-A
• chr11-62982208-T-C

Variant summary

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

The NM_153276.3(SLC22A6):​c.629-198A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 151,026 control chromosomes in the GnomAD database, including 6,220 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 0.26 (6220 hom., cov: 31)
• Consequence: SLC22A6 NM_153276.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.110

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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC22A6	NM_153276.3	c.629-198A>T		intron_variant		ENST00000360421.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC22A6	ENST00000360421.9	c.629-198A>T		intron_variant		1	NM_153276.3	P1

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39782 AN: 150978 Hom.: 6221 Cov.: 31

Gnomad AFR AF: 0.0985

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.263 AC: 39793 AN: 151026 Hom.: 6220 Cov.: 31 AF XY: 0.261 AC XY: 19221 AN XY: 73728

Gnomad4 AFR AF: 0.0985

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.143

Gnomad4 SAS AF: 0.205

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.361

Gnomad4 OTH AF: 0.272

Alfa AF: 0.317 Hom.: 1224

Bravo AF: 0.250

Asia WGS AF: 0.186 AC: 650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.3
DANN	Benign	0.45

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: rs6591722; hg19: chr11-62749680;