ENST00000659856.1:n.516+12389G>A

Variant names:

• chr20-60633776-G-A
• rs1150438
• ENST00000659856.1:n.516+12389G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000659856.1(MIR646HG):​n.516+12389G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,076 control chromosomes in the GnomAD database, including 3,132 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 0.18 (3132 hom., cov: 32)
• Consequence: MIR646HG ENST00000659856.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.665

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.248 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR646HG	ENST00000659856.1	n.516+12389G>A		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27031 AN: 151960 Hom.: 3135 Cov.: 32

Gnomad AFR AF: 0.0433

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.178 AC: 27019 AN: 152076 Hom.: 3132 Cov.: 32 AF XY: 0.179 AC XY: 13287 AN XY: 74342

Gnomad4 AFR AF: 0.0431

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.161

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.302

Gnomad4 NFE AF: 0.251

Gnomad4 OTH AF: 0.167

Alfa AF: 0.229 Hom.: 5610

Bravo AF: 0.158

Asia WGS AF: 0.145 AC: 504 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.4
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1150438; hg19: chr20-59208834;