ENST00000421257.1:n.36-44040G>A

Variant names:

• chr20-60269270-G-A
• rs6027452
• ENST00000421257.1:n.36-44040G>A

Variant summary

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

The ENST00000421257.1(MIR646HG):​n.36-44040G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,112 control chromosomes in the GnomAD database, including 3,410 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 0.16 (3410 hom., cov: 32)
• Consequence: MIR646HG ENST00000421257.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.68
• Publications: 2 publications found

Genes affected

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

LOC105372698 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.362 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR646HG	NR_046099.1		n.333-49651G>A		intron	N/A
	LOC105372698	NR_171673.1		n.63+13417G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR646HG	ENST00000421257.1	TSL:3	n.36-44040G>A		intron	N/A
	MIR646HG	ENST00000432910.5	TSL:2	n.333-49651G>A		intron	N/A
	MIR646HG	ENST00000437035.5	TSL:5	n.37-44040G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24713 AN: 151994 Hom.: 3384 Cov.: 32

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.0522

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.0695

Gnomad FIN AF: 0.0899

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0580

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.163 AC: 24804 AN: 152112 Hom.: 3410 Cov.: 32 AF XY: 0.162 AC XY: 12067 AN XY: 74372

African (AFR) AF: 0.367 AC: 15210 AN: 41456

American (AMR) AF: 0.185 AC: 2834 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0522 AC: 181 AN: 3466

East Asian (EAS) AF: 0.199 AC: 1028 AN: 5154

South Asian (SAS) AF: 0.0695 AC: 335 AN: 4818

European-Finnish (FIN) AF: 0.0899 AC: 953 AN: 10598

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0580 AC: 3943 AN: 68010

Other (OTH) AF: 0.141 AC: 298 AN: 2112

Alfa AF: 0.0886 Hom.: 716

Bravo AF: 0.180

Asia WGS AF: 0.154 AC: 533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.0070
DANN	Benign	0.38
PhyloP100		-3.7

Splicing

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

Other links and lift over

dbSNP: rs6027452; hg19: chr20-58844328;