rs270608

Positions:

• chr5-132312713-C-T

Variant summary

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

The NM_003059.3(SLC22A4):​c.497+449C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.712 in 152,166 control chromosomes in the GnomAD database, including 39,404 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 (39404 hom., cov: 33)
• Consequence: SLC22A4 NM_003059.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.289

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.84 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC22A4	NM_003059.3	c.497+449C>T		intron_variant		ENST00000200652.4
MIR3936HG	NR_110997.1	n.825-460G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC22A4	ENST00000200652.4	c.497+449C>T		intron_variant		1	NM_003059.3	P1
MIR3936HG	ENST00000621103.4	n.825-460G>A		intron_variant, non_coding_transcript_variant		1
SLC22A4	ENST00000491257.1	n.301+449C>T		intron_variant, non_coding_transcript_variant		4
MIR3936HG	ENST00000669845.1	n.451-460G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.712 AC: 108236 AN: 152048 Hom.: 39353 Cov.: 33

Gnomad AFR AF: 0.847

Gnomad AMI AF: 0.867

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.676

Gnomad EAS AF: 0.618

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.712 AC: 108343 AN: 152166 Hom.: 39404 Cov.: 33 AF XY: 0.700 AC XY: 52026 AN XY: 74372

Gnomad4 AFR AF: 0.847

Gnomad4 AMR AF: 0.707

Gnomad4 ASJ AF: 0.676

Gnomad4 EAS AF: 0.618

Gnomad4 SAS AF: 0.433

Gnomad4 FIN AF: 0.553

Gnomad4 NFE AF: 0.682

Gnomad4 OTH AF: 0.713

Alfa AF: 0.692 Hom.: 4570

Bravo AF: 0.737

Asia WGS AF: 0.528 AC: 1838 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.055
DANN	Benign	0.20

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: rs270608; hg19: chr5-131648406;