rs272842

chr5-132320824-A-Gchr5-132320824-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.653-1360A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.597 in 152,084 control chromosomes in the GnomAD database, including 27,737 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 0.60 (27736 hom., cov: 33)
  • Exomes 𝑓: 0.50 (1 hom.)
• Consequence: SLC22A4 NM_003059.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.286

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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC22A4	NM_003059.3	c.653-1360A>G		intron_variant		ENST00000200652.4
MIR3936HG	NR_110997.1	n.825-8571T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC22A4	ENST00000200652.4	c.653-1360A>G		intron_variant		1	NM_003059.3	P1
MIR3936HG	ENST00000621103.4	n.825-8571T>C		intron_variant, non_coding_transcript_variant		1
SLC22A4	ENST00000491257.1	n.457-41A>G		intron_variant, non_coding_transcript_variant		4
MIR3936HG	ENST00000669845.1	n.451-8571T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.597 AC: 90784 AN: 151958 Hom.: 27707 Cov.: 33

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.760

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.610

GnomAD4 exome AF: 0.500 AC: 4 AN: 8 Hom.: 1 Cov.: 0 AF XY: 0.500 AC XY: 4 AN XY: 8

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.598 AC: 90866 AN: 152076 Hom.: 27736 Cov.: 33 AF XY: 0.586 AC XY: 43598 AN XY: 74340

Gnomad4 AFR AF: 0.655

Gnomad4 AMR AF: 0.649

Gnomad4 ASJ AF: 0.585

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.358

Gnomad4 FIN AF: 0.487

Gnomad4 NFE AF: 0.604

Gnomad4 OTH AF: 0.610

Alfa AF: 0.607 Hom.: 37694

Bravo AF: 0.619

Asia WGS AF: 0.383 AC: 1335 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	9.7
Dann	Benign	0.84

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: rs272842; hg19: chr5-131656517;