rs272887

Positions:

• chr5-132330020-A-G
• chr5-132330020-A-T

Variant summary

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

The NM_003059.3(SLC22A4):​c.952-1736A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.707 in 152,084 control chromosomes in the GnomAD database, including 38,532 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 0.71 (38532 hom., cov: 32)
• Consequence: SLC22A4 NM_003059.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.542

Genes affected

SLC22A4 (HGNC:10968): (solute carrier family 22 member 4) Polyspecific organic cation transporters in the liver, kidney, intestine, and other organs are critical for elimination of many endogenous small organic cations as well as a wide array of drugs and environmental toxins. The encoded protein is an organic cation transporter and plasma integral membrane protein containing eleven putative transmembrane domains as well as a nucleotide-binding site motif. Transport by this protein is at least partially ATP-dependent. [provided by RefSeq, Jul 2008]

MIR3936HG (HGNC:40538): (MIR3936 host gene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.801 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC22A4	NM_003059.3	c.952-1736A>G		intron_variant		ENST00000200652.4	NP_003050.2
MIR3936HG	NR_110997.1	n.824+2169T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC22A4	ENST00000200652.4	c.952-1736A>G		intron_variant		1	NM_003059.3	ENSP00000200652	P1
MIR3936HG	ENST00000621103.4	n.824+2169T>C		intron_variant, non_coding_transcript_variant		1
MIR3936HG	ENST00000669845.1	n.450+2169T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.707 AC: 107378 AN: 151966 Hom.: 38499 Cov.: 32

Gnomad AFR AF: 0.808

Gnomad AMI AF: 0.870

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.701

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.707 AC: 107466 AN: 152084 Hom.: 38532 Cov.: 32 AF XY: 0.695 AC XY: 51651 AN XY: 74346

Gnomad4 AFR AF: 0.808

Gnomad4 AMR AF: 0.709

Gnomad4 ASJ AF: 0.701

Gnomad4 EAS AF: 0.620

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.571

Gnomad4 NFE AF: 0.689

Gnomad4 OTH AF: 0.710

Alfa AF: 0.693 Hom.: 48234

Bravo AF: 0.729

Asia WGS AF: 0.527 AC: 1833 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.2
DANN	Benign	0.75

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: rs272887; hg19: chr5-131665713;