rs4499874

Variant names:

• chr5-160497028-T-C
• rs4499874
• ENST00000770454.1:n.537-19080T>C

Variant summary

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

The ENST00000770454.1(MIR3142HG):​n.537-19080T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 152,006 control chromosomes in the GnomAD database, including 8,721 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 0.32 (8721 hom., cov: 31)
• Consequence: MIR3142HG ENST00000770454.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.12
• Publications: 1 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.588 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	ENST00000770454.1	n.537-19080T>C		intron_variant	Intron 1 of 2
MIR3142HG	ENST00000770455.1	n.441+11478T>C		intron_variant	Intron 2 of 3
MIR3142HG	ENST00000770456.1	n.166-19080T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49055 AN: 151886 Hom.: 8710 Cov.: 31

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.323 AC: 49109 AN: 152006 Hom.: 8721 Cov.: 31 AF XY: 0.325 AC XY: 24180 AN XY: 74324

African (AFR) AF: 0.425 AC: 17633 AN: 41446

American (AMR) AF: 0.323 AC: 4927 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 736 AN: 3470

East Asian (EAS) AF: 0.606 AC: 3122 AN: 5152

South Asian (SAS) AF: 0.420 AC: 2029 AN: 4826

European-Finnish (FIN) AF: 0.223 AC: 2356 AN: 10582

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17415 AN: 67946

Other (OTH) AF: 0.341 AC: 716 AN: 2102

Alfa AF: 0.288 Hom.: 11030

Bravo AF: 0.332

Asia WGS AF: 0.500 AC: 1737 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.079
DANN	Benign	0.50
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs4499874; hg19: chr5-159924035;