20-60224343-T-G

Variant names:

• chr20-60224343-T-G
• rs2865793
• ENST00000421257.1:n.35+43430T>G

Variant summary

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

The ENST00000421257.1(MIR646HG):​n.35+43430T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 151,852 control chromosomes in the GnomAD database, including 9,829 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 0.34 (9829 hom., cov: 32)
• Consequence: MIR646HG ENST00000421257.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.933
• Publications: 3 publications found

Genes affected

MIR646HG (HGNC:27659): (MIR646 host gene)

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 (AFR) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000421257.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR646HG	NR_046099.1		n.332+43430T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR646HG	ENST00000421257.1	TSL:3	n.35+43430T>G		intron	N/A
	MIR646HG	ENST00000427820.1	TSL:5	n.27-22450T>G		intron	N/A
	MIR646HG	ENST00000431181.5	TSL:3	n.767-21695T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50800 AN: 151734 Hom.: 9791 Cov.: 32

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.335 AC: 50910 AN: 151852 Hom.: 9829 Cov.: 32 AF XY: 0.337 AC XY: 24998 AN XY: 74220

African (AFR) AF: 0.540 AC: 22330 AN: 41376

American (AMR) AF: 0.309 AC: 4722 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 848 AN: 3466

East Asian (EAS) AF: 0.260 AC: 1333 AN: 5132

South Asian (SAS) AF: 0.259 AC: 1245 AN: 4816

European-Finnish (FIN) AF: 0.344 AC: 3622 AN: 10538

Middle Eastern (MID) AF: 0.274 AC: 80 AN: 292

European-Non Finnish (NFE) AF: 0.234 AC: 15910 AN: 67946

Other (OTH) AF: 0.303 AC: 636 AN: 2102

Alfa AF: 0.279 Hom.: 13727

Bravo AF: 0.345

Asia WGS AF: 0.299 AC: 1042 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.3
DANN	Benign	0.76
PhyloP100		0.93

Splicing

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

Other links and lift over

dbSNP: rs2865793; hg19: chr20-58799401;