chr11-63008426-A-C

Variant names:

• chr11-63008426-A-C
• rs2187383
• NM_004254.4:c.333+6200T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004254.4(SLC22A8):​c.333+6200T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.648 in 152,048 control chromosomes in the GnomAD database, including 32,204 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 0.65 (32204 hom., cov: 31)
• Consequence: SLC22A8 NM_004254.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00900
• Publications: 7 publications found

Genes affected

SLC22A8 (HGNC:10972): (solute carrier family 22 member 8) This gene encodes a protein involved in the sodium-independent transport and excretion of organic anions, some of which are potentially toxic. The encoded protein is an integral membrane protein and appears to be localized to the basolateral membrane of the kidney. Multiple alternatively spliced transcript variants that encode different protein isoforms have been described for this gene. [provided by RefSeq, May 2010]

ENSG00000301851 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.75 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004254.4. 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
	SLC22A8	NM_004254.4	MANE Select	c.333+6200T>G		intron	N/A	NP_004245.2
	SLC22A8	NM_001184732.2		c.333+6200T>G		intron	N/A	NP_001171661.1
	SLC22A8	NM_001184733.2		c.60+6200T>G		intron	N/A	NP_001171662.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC22A8	ENST00000336232.7	TSL:1 MANE Select	c.333+6200T>G		intron	N/A	ENSP00000337335.2
	SLC22A8	ENST00000430500.6	TSL:1	c.333+6200T>G		intron	N/A	ENSP00000398548.2
	SLC22A8	ENST00000311438.12	TSL:1	c.333+6200T>G		intron	N/A	ENSP00000311463.8

Frequencies

GnomAD3 genomes AF: 0.648 AC: 98410 AN: 151930 Hom.: 32147 Cov.: 31

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.775

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.769

Gnomad SAS AF: 0.741

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.675

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.659

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

GnomAD4 genome AF: 0.648 AC: 98529 AN: 152048 Hom.: 32204 Cov.: 31 AF XY: 0.653 AC XY: 48547 AN XY: 74302

African (AFR) AF: 0.712 AC: 29507 AN: 41458

American (AMR) AF: 0.647 AC: 9896 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.678 AC: 2353 AN: 3470

East Asian (EAS) AF: 0.770 AC: 3977 AN: 5168

South Asian (SAS) AF: 0.740 AC: 3570 AN: 4824

European-Finnish (FIN) AF: 0.640 AC: 6761 AN: 10570

Middle Eastern (MID) AF: 0.678 AC: 198 AN: 292

European-Non Finnish (NFE) AF: 0.591 AC: 40159 AN: 67946

Other (OTH) AF: 0.663 AC: 1401 AN: 2114

Alfa AF: 0.610 Hom.: 46829

Bravo AF: 0.649

Asia WGS AF: 0.754 AC: 2620 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.3
DANN	Benign	0.75
PhyloP100		-0.0090
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: rs2187383; hg19: chr11-62775898;