11-64565824-A-G

Variant summary

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

The NM_018484.4(SLC22A11):c.1058+487A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.711 in 309,010 control chromosomes in the GnomAD database, including 79,071 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 0.73 (41071 hom., cov: 31)
  • Exomes 𝑓: 0.69 (38000 hom.)
• Consequence: SLC22A11 NM_018484.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.817

Genes affected

SLC22A11 (HGNC:18120): (solute carrier family 22 member 11) The protein encoded by this gene is 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 is found mainly in the kidney and in the placenta, where it may act to prevent potentially harmful organic anions from reaching the fetus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.834 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC22A11	NM_018484.4	c.1058+487A>G		intron_variant		ENST00000301891.9
SLC22A11	NM_001307985.2	c.1058+487A>G		intron_variant
SLC22A11	XM_011545167.2	c.659+487A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC22A11	ENST00000301891.9	c.1058+487A>G		intron_variant		1	NM_018484.4	P1

Frequencies

GnomAD3 genomes AF: 0.730 AC: 110957 AN: 151926 Hom.: 41017 Cov.: 31

Gnomad AFR AF: 0.841

Gnomad AMI AF: 0.648

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.670

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.699

GnomAD4 exome AF: 0.693 AC: 108756 AN: 156966 Hom.: 38000 Cov.: 0 AF XY: 0.692 AC XY: 58223 AN XY: 84162

Gnomad4 AFR exome AF: 0.848

Gnomad4 AMR exome AF: 0.711

Gnomad4 ASJ exome AF: 0.771

Gnomad4 EAS exome AF: 0.658

Gnomad4 SAS exome AF: 0.682

Gnomad4 FIN exome AF: 0.625

Gnomad4 NFE exome AF: 0.690

Gnomad4 OTH exome AF: 0.693

GnomAD4 genome AF: 0.730 AC: 111063 AN: 152044 Hom.: 41071 Cov.: 31 AF XY: 0.727 AC XY: 54036 AN XY: 74332

Gnomad4 AFR AF: 0.842

Gnomad4 AMR AF: 0.724

Gnomad4 ASJ AF: 0.774

Gnomad4 EAS AF: 0.670

Gnomad4 SAS AF: 0.650

Gnomad4 FIN AF: 0.626

Gnomad4 NFE AF: 0.690

Gnomad4 OTH AF: 0.693

Alfa AF: 0.696 Hom.: 61607

Bravo AF: 0.741

Asia WGS AF: 0.612 AC: 2129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.6
Dann	Benign	0.59

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: rs1783811; hg19: chr11-64333296;