rs3782099

Variant names:

• chr11-64560238-T-C
• rs3782099
• NM_018484.4:c.497+1000T>C

Variant summary

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

The NM_018484.4(SLC22A11):​c.497+1000T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 151,774 control chromosomes in the GnomAD database, including 16,261 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 0.45 (16261 hom., cov: 30)
• Consequence: SLC22A11 NM_018484.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.18
• Publications: 4 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=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC22A11	NM_018484.4	c.497+1000T>C		intron_variant	Intron 2 of 9	ENST00000301891.9	NP_060954.1
SLC22A11	NM_001307985.2	c.497+1000T>C		intron_variant	Intron 2 of 7		NP_001294914.1
SLC22A11	XM_011545167.2	c.99-1766T>C		intron_variant	Intron 1 of 8		XP_011543469.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC22A11	ENST00000301891.9	c.497+1000T>C		intron_variant	Intron 2 of 9	1	NM_018484.4	ENSP00000301891.4

Frequencies

GnomAD3 genomes AF: 0.448 AC: 67916 AN: 151656 Hom.: 16252 Cov.: 30

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.0569

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.448 AC: 67964 AN: 151774 Hom.: 16261 Cov.: 30 AF XY: 0.439 AC XY: 32586 AN XY: 74168

African (AFR) AF: 0.374 AC: 15447 AN: 41336

American (AMR) AF: 0.358 AC: 5464 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.538 AC: 1864 AN: 3462

East Asian (EAS) AF: 0.0569 AC: 293 AN: 5152

South Asian (SAS) AF: 0.381 AC: 1827 AN: 4798

European-Finnish (FIN) AF: 0.442 AC: 4671 AN: 10568

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.542 AC: 36820 AN: 67876

Other (OTH) AF: 0.431 AC: 909 AN: 2110

Alfa AF: 0.488 Hom.: 2328

Bravo AF: 0.438

Asia WGS AF: 0.213 AC: 742 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	0.14
DANN	Benign	0.23
PhyloP100		-2.2
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs3782099; hg19: chr11-64327710;