rs13179900

Variant names:

• chr5-132311897-G-A
• rs13179900
• ENST00000621103.4:n.1181C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-132311897-G-A
• chr5-132311897-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000621103.4(MIR3936HG):​n.1181C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.083 in 553,826 control chromosomes in the GnomAD database, including 2,820 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 0.075 (548 hom., cov: 33)
  • Exomes 𝑓: 0.086 (2272 hom.)
• Consequence: MIR3936HG ENST00000621103.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.248
• Publications: 8 publications found

Genes affected

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

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC22A4	NM_003059.3	c.394-264G>A		intron_variant	Intron 1 of 9	ENST00000200652.4	NP_003050.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR3936HG	ENST00000621103.4	n.1181C>T		non_coding_transcript_exon_variant	Exon 8 of 8	1
SLC22A4	ENST00000200652.4	c.394-264G>A		intron_variant	Intron 1 of 9	1	NM_003059.3	ENSP00000200652.3
MIR3936HG	ENST00000669845.1	n.807C>T		non_coding_transcript_exon_variant	Exon 4 of 4
SLC22A4	ENST00000491257.1	n.198-264G>A		intron_variant	Intron 1 of 3	4

Frequencies

GnomAD3 genomes AF: 0.0753 AC: 11457 AN: 152110 Hom.: 551 Cov.: 33

Gnomad AFR AF: 0.0567

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.0488

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.0650

Gnomad FIN AF: 0.0750

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0766

Gnomad OTH AF: 0.0747

GnomAD4 exome AF: 0.0859 AC: 34505 AN: 401598 Hom.: 2272 Cov.: 0 AF XY: 0.0845 AC XY: 17844 AN XY: 211234

African (AFR) AF: 0.0557 AC: 638 AN: 11454

American (AMR) AF: 0.0388 AC: 680 AN: 17540

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 1321 AN: 12350

East Asian (EAS) AF: 0.297 AC: 8041 AN: 27104

South Asian (SAS) AF: 0.0512 AC: 2305 AN: 44982

European-Finnish (FIN) AF: 0.0735 AC: 1859 AN: 25302

Middle Eastern (MID) AF: 0.0625 AC: 110 AN: 1760

European-Non Finnish (NFE) AF: 0.0741 AC: 17631 AN: 237886

Other (OTH) AF: 0.0827 AC: 1920 AN: 23220

GnomAD4 genome AF: 0.0753 AC: 11457 AN: 152228 Hom.: 548 Cov.: 33 AF XY: 0.0744 AC XY: 5534 AN XY: 74426

African (AFR) AF: 0.0567 AC: 2357 AN: 41548

American (AMR) AF: 0.0487 AC: 745 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 377 AN: 3470

East Asian (EAS) AF: 0.268 AC: 1383 AN: 5164

South Asian (SAS) AF: 0.0649 AC: 313 AN: 4826

European-Finnish (FIN) AF: 0.0750 AC: 795 AN: 10600

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

European-Non Finnish (NFE) AF: 0.0766 AC: 5211 AN: 68004

Other (OTH) AF: 0.0749 AC: 158 AN: 2110

Alfa AF: 0.0749 Hom.: 1813

Bravo AF: 0.0727

Asia WGS AF: 0.122 AC: 425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.4
DANN	Benign	0.36
PhyloP100		0.25
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: rs13179900; hg19: chr5-131647590; COSMIC: COSV52358926;