rs270607

Variant names:

• chr5-132313493-A-G
• rs270607
• NM_003059.3:c.498-121A>G

Your query was ambiguous. Multiple possible variants found:

• chr5-132313493-A-G
• chr5-132313493-A-C
• chr5-132313493-A-T

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.498-121A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.663 in 875,446 control chromosomes in the GnomAD database, including 195,674 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.69 (36432 hom., cov: 33)
  • Exomes 𝑓: 0.66 (159242 hom.)
• Consequence: SLC22A4 NM_003059.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0980
• Publications: 19 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=-0.91).
• BP6: Variant 5-132313493-A-G is Benign according to our data. Variant chr5-132313493-A-G is described in ClinVar as Benign. ClinVar VariationId is 1220625.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.756 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.498-121A>G		intron	N/A	NP_003050.2
	MIR3936HG	NR_110997.1		n.825-1240T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC22A4	ENST00000200652.4	TSL:1 MANE Select	c.498-121A>G		intron	N/A	ENSP00000200652.3	Q9H015
	MIR3936HG	ENST00000621103.4	TSL:1	n.825-1240T>C		intron	N/A
	SLC22A4	ENST00000947750.1		c.498-121A>G		intron	N/A	ENSP00000617809.1

Frequencies

GnomAD3 genomes AF: 0.688 AC: 104597 AN: 151974 Hom.: 36401 Cov.: 33

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.870

Gnomad AMR AF: 0.702

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.680

Gnomad OTH AF: 0.693

GnomAD4 exome AF: 0.658 AC: 475814 AN: 723354 Hom.: 159242 AF XY: 0.646 AC XY: 250412 AN XY: 387366

African (AFR) AF: 0.760 AC: 14736 AN: 19384

American (AMR) AF: 0.713 AC: 31140 AN: 43648

Ashkenazi Jewish (ASJ) AF: 0.714 AC: 15184 AN: 21252

East Asian (EAS) AF: 0.636 AC: 23168 AN: 36414

South Asian (SAS) AF: 0.439 AC: 30911 AN: 70480

European-Finnish (FIN) AF: 0.567 AC: 28390 AN: 50058

Middle Eastern (MID) AF: 0.604 AC: 1849 AN: 3062

European-Non Finnish (NFE) AF: 0.692 AC: 306381 AN: 442924

Other (OTH) AF: 0.666 AC: 24055 AN: 36132

GnomAD4 genome AF: 0.688 AC: 104682 AN: 152092 Hom.: 36432 Cov.: 33 AF XY: 0.677 AC XY: 50335 AN XY: 74346

African (AFR) AF: 0.763 AC: 31646 AN: 41498

American (AMR) AF: 0.702 AC: 10722 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.699 AC: 2426 AN: 3470

East Asian (EAS) AF: 0.620 AC: 3201 AN: 5164

South Asian (SAS) AF: 0.437 AC: 2105 AN: 4820

European-Finnish (FIN) AF: 0.561 AC: 5939 AN: 10578

Middle Eastern (MID) AF: 0.599 AC: 175 AN: 292

European-Non Finnish (NFE) AF: 0.680 AC: 46215 AN: 67972

Other (OTH) AF: 0.693 AC: 1460 AN: 2108

Alfa AF: 0.688 Hom.: 44387

Bravo AF: 0.709

Asia WGS AF: 0.524 AC: 1825 AN: 3478

ClinVar

ClinVar submissions

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	-0.91
CADD	Benign	3.5
DANN	Benign	0.74
PhyloP100		-0.098
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: rs270607; hg19: chr5-131649186; COSMIC: COSV52356677;