11-64566642-C-T

Variant names:

• chr11-64566642-C-T
• rs2078267
• NM_018484.4:c.1059-957C>T

Variant summary

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

The NM_018484.4(SLC22A11):​c.1059-957C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 151,998 control chromosomes in the GnomAD database, including 12,775 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 0.37 (12762 hom., cov: 31)
  • Exomes 𝑓: 0.37 (13 hom.)
• Consequence: SLC22A11 NM_018484.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.858

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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC22A11	NM_018484.4	c.1059-957C>T		intron_variant	Intron 6 of 9	ENST00000301891.9	NP_060954.1
SLC22A11	NM_001307985.2	c.1058+1305C>T		intron_variant	Intron 6 of 7		NP_001294914.1
SLC22A11	XM_011545167.2	c.660-957C>T		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.1059-957C>T		intron_variant	Intron 6 of 9	1	NM_018484.4	ENSP00000301891.4
SLC22A11	ENST00000377581.7	c.1059-957C>T		intron_variant	Intron 6 of 8	5		ENSP00000366804.3
SLC22A11	ENST00000377585.7	c.1058+1305C>T		intron_variant	Intron 6 of 7	2		ENSP00000366809.3
SLC22A11	ENST00000460745.1	n.1788C>T		non_coding_transcript_exon_variant	Exon 4 of 4	2

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55653 AN: 151724 Hom.: 12767 Cov.: 31

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.0199

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.372

GnomAD4 exome AF: 0.370 AC: 57 AN: 154 Hom.: 13 Cov.: 0 AF XY: 0.311 AC XY: 23 AN XY: 74

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.333

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.542

Gnomad4 NFE exome AF: 0.463

Gnomad4 OTH exome AF: 0.400

GnomAD4 genome AF: 0.366 AC: 55649 AN: 151844 Hom.: 12762 Cov.: 31 AF XY: 0.361 AC XY: 26762 AN XY: 74182

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.315

Gnomad4 ASJ AF: 0.534

Gnomad4 EAS AF: 0.0200

Gnomad4 SAS AF: 0.370

Gnomad4 FIN AF: 0.425

Gnomad4 NFE AF: 0.527

Gnomad4 OTH AF: 0.368

Alfa AF: 0.479 Hom.: 21345

Bravo AF: 0.345

Asia WGS AF: 0.169 AC: 588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.8
DANN	Benign	0.86

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: rs2078267; hg19: chr11-64334114;