rs17729021

Variant names:

• chr20-60487044-A-G
• rs17729021
• ENST00000437035.5:n.428-40343A>G

Variant summary

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

The ENST00000437035.5(MIR646HG):​n.428-40343A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,076 control chromosomes in the GnomAD database, including 3,088 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 0.19 (3088 hom., cov: 33)
• Consequence: MIR646HG ENST00000437035.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.665
• Publications: 4 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000437035.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR646HG	ENST00000437035.5	TSL:5	n.428-40343A>G		intron	N/A
	MIR646HG	ENST00000659856.1		n.354-40343A>G		intron	N/A
	MIR646HG	ENST00000665114.1		n.359-40343A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29602 AN: 151958 Hom.: 3086 Cov.: 33

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.195 AC: 29604 AN: 152076 Hom.: 3088 Cov.: 33 AF XY: 0.192 AC XY: 14275 AN XY: 74326

African (AFR) AF: 0.134 AC: 5552 AN: 41496

American (AMR) AF: 0.140 AC: 2139 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 654 AN: 3470

East Asian (EAS) AF: 0.135 AC: 697 AN: 5156

South Asian (SAS) AF: 0.170 AC: 819 AN: 4816

European-Finnish (FIN) AF: 0.260 AC: 2748 AN: 10570

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.240 AC: 16299 AN: 67960

Other (OTH) AF: 0.203 AC: 429 AN: 2112

Alfa AF: 0.219 Hom.: 6487

Bravo AF: 0.181

Asia WGS AF: 0.154 AC: 535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.36
DANN	Benign	0.67
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs17729021; hg19: chr20-59062102;