11-64555608-C-T

Variant names:

• chr11-64555608-C-T
• rs3759053
• ENST00000377585.7:c.-392C>T

Variant summary

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

The ENST00000377585.7(SLC22A11):​c.-392C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 186,428 control chromosomes in the GnomAD database, including 19,684 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 0.43 (15493 hom., cov: 32)
  • Exomes 𝑓: 0.47 (4191 hom.)
• Consequence: SLC22A11 ENST00000377585.7 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 10 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000377585.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC22A11	ENST00000377585.7	TSL:2	c.-392C>T		upstream_gene	N/A	ENSP00000366809.3	Q9NSA0-2

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65303 AN: 151978 Hom.: 15493 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.583

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.0560

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.428

GnomAD4 exome AF: 0.466 AC: 15990 AN: 34332 Hom.: 4191 Cov.: 0 AF XY: 0.469 AC XY: 8232 AN XY: 17560

African (AFR) AF: 0.297 AC: 409 AN: 1378

American (AMR) AF: 0.318 AC: 1002 AN: 3148

Ashkenazi Jewish (ASJ) AF: 0.538 AC: 593 AN: 1102

East Asian (EAS) AF: 0.0720 AC: 174 AN: 2416

South Asian (SAS) AF: 0.405 AC: 626 AN: 1544

European-Finnish (FIN) AF: 0.418 AC: 522 AN: 1248

Middle Eastern (MID) AF: 0.515 AC: 67 AN: 130

European-Non Finnish (NFE) AF: 0.546 AC: 11634 AN: 21292

Other (OTH) AF: 0.464 AC: 963 AN: 2074

GnomAD4 genome AF: 0.429 AC: 65320 AN: 152096 Hom.: 15493 Cov.: 32 AF XY: 0.422 AC XY: 31379 AN XY: 74342

African (AFR) AF: 0.293 AC: 12175 AN: 41502

American (AMR) AF: 0.350 AC: 5349 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.548 AC: 1901 AN: 3470

East Asian (EAS) AF: 0.0560 AC: 290 AN: 5182

South Asian (SAS) AF: 0.383 AC: 1842 AN: 4812

European-Finnish (FIN) AF: 0.456 AC: 4820 AN: 10560

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

European-Non Finnish (NFE) AF: 0.550 AC: 37372 AN: 67976

Other (OTH) AF: 0.425 AC: 897 AN: 2110

Alfa AF: 0.504 Hom.: 79243

Bravo AF: 0.415

Asia WGS AF: 0.201 AC: 701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.14
DANN	Benign	0.33
PhyloP100		-1.2
PromoterAI		0.044	Neutral

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3759053; hg19: chr11-64323080;