chr20-60321657-A-G

Variant names:

• chr20-60321657-A-G
• rs6027506
• ENST00000432910.5:n.1444A>G

Variant summary

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

The ENST00000432910.5(MIR646HG):​n.1444A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 151,274 control chromosomes in the GnomAD database, including 12,892 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 0.40 (12892 hom., cov: 28)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MIR646HG ENST00000432910.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.294
• Publications: 7 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000432910.5. 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
	MIR646HG	NR_046099.1		n.1444A>G		non_coding_transcript_exon	Exon 5 of 5

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR646HG	ENST00000432910.5	TSL:2	n.1444A>G		non_coding_transcript_exon	Exon 5 of 5
	MIR646HG	ENST00000663127.1		n.114A>G		non_coding_transcript_exon	Exon 1 of 2
	MIR646HG	ENST00000421257.1	TSL:3	n.113+8270A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.397 AC: 59939 AN: 151158 Hom.: 12855 Cov.: 28

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.328

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.376

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.397 AC: 60034 AN: 151274 Hom.: 12892 Cov.: 28 AF XY: 0.391 AC XY: 28876 AN XY: 73906

African (AFR) AF: 0.560 AC: 23014 AN: 41082

American (AMR) AF: 0.289 AC: 4401 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.424 AC: 1470 AN: 3470

East Asian (EAS) AF: 0.101 AC: 522 AN: 5154

South Asian (SAS) AF: 0.300 AC: 1433 AN: 4784

European-Finnish (FIN) AF: 0.395 AC: 4123 AN: 10446

Middle Eastern (MID) AF: 0.342 AC: 100 AN: 292

European-Non Finnish (NFE) AF: 0.352 AC: 23876 AN: 67828

Other (OTH) AF: 0.380 AC: 796 AN: 2092

Alfa AF: 0.377 Hom.: 14096

Bravo AF: 0.394

Asia WGS AF: 0.263 AC: 919 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.3
DANN	Benign	0.34
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs6027506; hg19: chr20-58896715;