rs2431099

Variant names:

• chr5-160459613-A-G
• rs2431099
• ENST00000642173.1:n.76+20944A>G

Your query was ambiguous. Multiple possible variants found:

• chr5-160459613-A-G
• chr5-160459613-A-T

Variant summary

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

The ENST00000642173.1(MIR3142HG):​n.76+20944A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.507 in 152,030 control chromosomes in the GnomAD database, including 19,704 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 0.51 (19704 hom., cov: 32)
• Consequence: MIR3142HG ENST00000642173.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610
• Publications: 21 publications found

Genes affected

MIR3142HG (HGNC:51944): (MIR3142 host gene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR3142HG	ENST00000642173.1	n.76+20944A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.507 AC: 76976 AN: 151912 Hom.: 19692 Cov.: 32

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.633

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.507 AC: 77036 AN: 152030 Hom.: 19704 Cov.: 32 AF XY: 0.507 AC XY: 37697 AN XY: 74322

African (AFR) AF: 0.470 AC: 19463 AN: 41434

American (AMR) AF: 0.493 AC: 7526 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1618 AN: 3470

East Asian (EAS) AF: 0.633 AC: 3272 AN: 5170

South Asian (SAS) AF: 0.496 AC: 2390 AN: 4820

European-Finnish (FIN) AF: 0.540 AC: 5706 AN: 10566

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.523 AC: 35528 AN: 67976

Other (OTH) AF: 0.523 AC: 1103 AN: 2108

Alfa AF: 0.515 Hom.: 87151

Bravo AF: 0.499

Asia WGS AF: 0.581 AC: 2016 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.71
DANN	Benign	0.54
PhyloP100		-0.061

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2431099; hg19: chr5-159886620;