11-64565824-A-G

Variant names:

• chr11-64565824-A-G
• rs1783811
• NM_018484.4:c.1058+487A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 18 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SLC22A11	NM_018484.4	c.1058+487A>G		intron_variant	Intron 6 of 9	ENST00000301891.9	NP_060954.1
SLC22A11	NM_001307985.2	c.1058+487A>G		intron_variant	Intron 6 of 7		NP_001294914.1
SLC22A11	XM_011545167.2	c.659+487A>G		intron_variant	Intron 5 of 8		XP_011543469.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC22A11	ENST00000301891.9	c.1058+487A>G		intron_variant	Intron 6 of 9	1	NM_018484.4	ENSP00000301891.4

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

African (AFR) AF: 0.848 AC: 4159 AN: 4904

American (AMR) AF: 0.711 AC: 7189 AN: 10118

Ashkenazi Jewish (ASJ) AF: 0.771 AC: 2815 AN: 3652

East Asian (EAS) AF: 0.658 AC: 5056 AN: 7682

South Asian (SAS) AF: 0.682 AC: 20019 AN: 29370

European-Finnish (FIN) AF: 0.625 AC: 4091 AN: 6550

Middle Eastern (MID) AF: 0.750 AC: 791 AN: 1054

European-Non Finnish (NFE) AF: 0.690 AC: 59141 AN: 85712

Other (OTH) AF: 0.693 AC: 5495 AN: 7924

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

African (AFR) AF: 0.842 AC: 34924 AN: 41496

American (AMR) AF: 0.724 AC: 11061 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.774 AC: 2686 AN: 3470

East Asian (EAS) AF: 0.670 AC: 3462 AN: 5170

South Asian (SAS) AF: 0.650 AC: 3131 AN: 4814

European-Finnish (FIN) AF: 0.626 AC: 6609 AN: 10556

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.690 AC: 46911 AN: 67940

Other (OTH) AF: 0.693 AC: 1460 AN: 2106

Alfa AF: 0.703 Hom.: 154192

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
PhyloP100		0.82
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: rs1783811; hg19: chr11-64333296;