20-60137401-G-A

Variant names:

• chr20-60137401-G-A
• rs6092877
• ENST00000427691.5:n.360+16280G>A

Variant summary

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

The ENST00000427691.5(MIR646HG):​n.360+16280G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.096 in 152,234 control chromosomes in the GnomAD database, including 1,771 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 0.096 (1771 hom., cov: 33)
• Consequence: MIR646HG ENST00000427691.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280
• Publications: 1 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000427691.5. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR646HG	ENST00000427691.5	TSL:3	n.360+16280G>A		intron	N/A
	MIR646HG	ENST00000431181.5	TSL:3	n.766+13541G>A		intron	N/A
	MIR646HG	ENST00000458422.6	TSL:3	n.278+16280G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0959 AC: 14583 AN: 152116 Hom.: 1765 Cov.: 33

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0627

Gnomad ASJ AF: 0.0565

Gnomad EAS AF: 0.0965

Gnomad SAS AF: 0.0350

Gnomad FIN AF: 0.00245

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0123

Gnomad OTH AF: 0.0874

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

GnomAD4 genome AF: 0.0960 AC: 14608 AN: 152234 Hom.: 1771 Cov.: 33 AF XY: 0.0934 AC XY: 6951 AN XY: 74440

African (AFR) AF: 0.282 AC: 11704 AN: 41504

American (AMR) AF: 0.0626 AC: 957 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0565 AC: 196 AN: 3468

East Asian (EAS) AF: 0.0967 AC: 500 AN: 5168

South Asian (SAS) AF: 0.0350 AC: 169 AN: 4828

European-Finnish (FIN) AF: 0.00245 AC: 26 AN: 10620

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0123 AC: 838 AN: 68026

Other (OTH) AF: 0.0870 AC: 184 AN: 2116

Alfa AF: 0.0614 Hom.: 152

Bravo AF: 0.109

Asia WGS AF: 0.0680 AC: 235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.4
DANN	Benign	0.37
PhyloP100		-0.028

Splicing

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

Other links and lift over

dbSNP: rs6092877; hg19: chr20-58712457;