chr5-132313529-G-A

Variant names:

• chr5-132313529-G-A
• rs2073838
• NM_003059.3:c.498-85G>A

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_003059.3(SLC22A4):​c.498-85G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0786 in 1,244,976 control chromosomes in the GnomAD database, including 5,114 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.073 (540 hom., cov: 33)
  • Exomes 𝑓: 0.079 (4574 hom.)
• Consequence: SLC22A4 NM_003059.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.128
• Publications: 27 publications found

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

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP6: Variant 5-132313529-G-A is Benign according to our data. Variant chr5-132313529-G-A is described in ClinVar as Benign. ClinVar VariationId is 1280356.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003059.3. 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
	SLC22A4	NM_003059.3	MANE Select	c.498-85G>A		intron	N/A	NP_003050.2
	MIR3936HG	NR_110997.1		n.825-1276C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC22A4	ENST00000200652.4	TSL:1 MANE Select	c.498-85G>A		intron	N/A	ENSP00000200652.3	Q9H015
	MIR3936HG	ENST00000621103.4	TSL:1	n.825-1276C>T		intron	N/A
	SLC22A4	ENST00000947750.1		c.498-85G>A		intron	N/A	ENSP00000617809.1

Frequencies

GnomAD3 genomes AF: 0.0728 AC: 11080 AN: 152166 Hom.: 543 Cov.: 33

Gnomad AFR AF: 0.0483

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.0479

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.0650

Gnomad FIN AF: 0.0752

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0765

Gnomad OTH AF: 0.0731

GnomAD4 exome AF: 0.0794 AC: 86719 AN: 1092692 Hom.: 4574 AF XY: 0.0787 AC XY: 44149 AN XY: 560848

African (AFR) AF: 0.0453 AC: 1191 AN: 26276

American (AMR) AF: 0.0330 AC: 1461 AN: 44286

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 2562 AN: 23784

East Asian (EAS) AF: 0.293 AC: 11126 AN: 37968

South Asian (SAS) AF: 0.0523 AC: 4108 AN: 78530

European-Finnish (FIN) AF: 0.0758 AC: 4026 AN: 53110

Middle Eastern (MID) AF: 0.0631 AC: 292 AN: 4624

European-Non Finnish (NFE) AF: 0.0749 AC: 58096 AN: 775926

Other (OTH) AF: 0.0800 AC: 3857 AN: 48188

GnomAD4 genome AF: 0.0728 AC: 11079 AN: 152284 Hom.: 540 Cov.: 33 AF XY: 0.0720 AC XY: 5362 AN XY: 74448

African (AFR) AF: 0.0483 AC: 2007 AN: 41562

American (AMR) AF: 0.0478 AC: 732 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 364 AN: 3472

East Asian (EAS) AF: 0.268 AC: 1388 AN: 5172

South Asian (SAS) AF: 0.0648 AC: 313 AN: 4828

European-Finnish (FIN) AF: 0.0752 AC: 798 AN: 10608

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0765 AC: 5204 AN: 68022

Other (OTH) AF: 0.0733 AC: 155 AN: 2116

Alfa AF: 0.0722 Hom.: 696

Bravo AF: 0.0699

Asia WGS AF: 0.122 AC: 426 AN: 3478

ClinVar

ClinVar submissions as Germline

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.3
DANN	Benign	0.56
PhyloP100		0.13
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2073838; hg19: chr5-131649222; COSMIC: COSV52358934;