rs2961920

Variant names:

• chr5-160484499-C-A
• rs2961920
• ENST00000517927.2:n.311-800C>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000517927.2(MIR3142HG):​n.311-800C>A variant causes a intron 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 ENST00000517927.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62
• Publications: 16 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=-0.89).
• 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 rank	MANE	Protein	UniProt
MIR3142HG	NR_132748.1	n.191-800C>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR3142HG	ENST00000517927.2	n.311-800C>A		intron_variant	Intron 1 of 1	1
MIR3142HG	ENST00000642173.1	n.77-800C>A		intron_variant	Intron 1 of 1
MIR3142HG	ENST00000770454.1	n.536+16059C>A		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.603 AC: 24969 AN: 41430

American (AMR) AF: 0.708 AC: 10807 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.774 AC: 2683 AN: 3468

East Asian (EAS) AF: 0.376 AC: 1939 AN: 5156

South Asian (SAS) AF: 0.703 AC: 3378 AN: 4802

European-Finnish (FIN) AF: 0.787 AC: 8329 AN: 10578

Middle Eastern (MID) AF: 0.634 AC: 185 AN: 292

European-Non Finnish (NFE) AF: 0.765 AC: 51970 AN: 67942

Other (OTH) AF: 0.686 AC: 1447 AN: 2108

Alfa AF: 0.740 Hom.: 142115

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
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs2961920; hg19: chr5-159911506;