rs17300741

chr11-64563990-A-Gchr11-64563990-A-T

Variant summary

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

The NM_018484.4(SLC22A11):c.822-318A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.438 in 151,860 control chromosomes in the GnomAD database, including 15,579 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 0.44 (15579 hom., cov: 31)
• Consequence: SLC22A11 NM_018484.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30

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=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC22A11	NM_018484.4	c.822-318A>G		intron_variant		ENST00000301891.9
SLC22A11	NM_001307985.2	c.822-318A>G		intron_variant
SLC22A11	XM_011545167.2	c.423-318A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC22A11	ENST00000301891.9	c.822-318A>G		intron_variant		1	NM_018484.4	P1

Frequencies

GnomAD3 genomes AF: 0.439 AC: 66541 AN: 151742 Hom.: 15570 Cov.: 31

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.0574

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.438 AC: 66589 AN: 151860 Hom.: 15579 Cov.: 31 AF XY: 0.431 AC XY: 31999 AN XY: 74236

Gnomad4 AFR AF: 0.370

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.538

Gnomad4 EAS AF: 0.0576

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.429

Gnomad4 NFE AF: 0.529

Gnomad4 OTH AF: 0.424

Alfa AF: 0.498 Hom.: 35511

Bravo AF: 0.428

Asia WGS AF: 0.210 AC: 732 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.21
Dann	Benign	0.32

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: rs17300741; hg19: chr11-64331462;