rs2961920

Positions:

• chr5-160484499-C-A
• chr5-160484499-C-G

Variant summary

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

The NR_132748.1(MIR3142HG):​n.191-800C>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.7 in 151,952 control chromosomes in the GnomAD database, including 37,863 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 0.70 (37863 hom., cov: 30)
• Consequence: MIR3142HG NR_132748.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR3142HG	NR_132748.1	n.191-800C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR3142HG	ENST00000517927.1	n.174-800C>A		intron_variant, non_coding_transcript_variant		1
MIR3142HG	ENST00000642173.1	n.77-800C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.700 AC: 106257 AN: 151834 Hom.: 37837 Cov.: 30

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.704

Gnomad FIN AF: 0.787

Gnomad MID AF: 0.634

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.685

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

GnomAD4 genome AF: 0.700 AC: 106329 AN: 151952 Hom.: 37863 Cov.: 30 AF XY: 0.700 AC XY: 52007 AN XY: 74266

Gnomad4 AFR AF: 0.603

Gnomad4 AMR AF: 0.708

Gnomad4 ASJ AF: 0.774

Gnomad4 EAS AF: 0.376

Gnomad4 SAS AF: 0.703

Gnomad4 FIN AF: 0.787

Gnomad4 NFE AF: 0.765

Gnomad4 OTH AF: 0.686

Alfa AF: 0.751 Hom.: 89040

Bravo AF: 0.688

Asia WGS AF: 0.547 AC: 1906 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.014
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2961920; hg19: chr5-159911506;