rs6591722

Variant names:

• chr11-62982208-T-A
• rs6591722
• NM_153276.3:c.629-198A>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 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=-0.81).
• 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 rank	MANE	Protein	UniProt
SLC22A6	NM_153276.3	c.629-198A>T		intron_variant	Intron 3 of 9	ENST00000360421.9	NP_695008.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC22A6	ENST00000360421.9	c.629-198A>T		intron_variant	Intron 3 of 9	1	NM_153276.3	ENSP00000353597.4

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

African (AFR) AF: 0.0985 AC: 4052 AN: 41134

American (AMR) AF: 0.283 AC: 4299 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 980 AN: 3462

East Asian (EAS) AF: 0.143 AC: 732 AN: 5136

South Asian (SAS) AF: 0.205 AC: 978 AN: 4782

European-Finnish (FIN) AF: 0.331 AC: 3372 AN: 10202

Middle Eastern (MID) AF: 0.290 AC: 84 AN: 290

European-Non Finnish (NFE) AF: 0.361 AC: 24499 AN: 67812

Other (OTH) AF: 0.272 AC: 570 AN: 2094

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
PhyloP100		0.11
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: rs6591722; hg19: chr11-62749680;