11-64566642-C-G

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_018484.4(SLC22A11):​c.1059-957C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: SLC22A11 NM_018484.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.858
• Publications: 0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.6
DANN	Benign	0.59
PhyloP100		-0.86

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs2078267; hg19: chr11-64334114;