rs1150438

chr20-60633776-G-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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR646HG	ENST00000659856.1	n.516+12389G>A		intron_variant, non_coding_transcript_variant

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;