rs6092877

chr20-60137401-G-A

Variant summary

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

The ENST00000427691.5(MIR646HG):n.360+16280G>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 0.096 in 152,234 control chromosomes in the GnomAD database, including 1,771 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 0.096 (1771 hom., cov: 33)
• Consequence: MIR646HG ENST00000427691.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280

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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.278 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	ENST00000427691.5	n.360+16280G>A		intron_variant, non_coding_transcript_variant		3
MIR646HG	ENST00000431181.5	n.766+13541G>A		intron_variant, non_coding_transcript_variant		3
MIR646HG	ENST00000458422.5	n.62+16280G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0959 AC: 14583 AN: 152116 Hom.: 1765 Cov.: 33

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0627

Gnomad ASJ AF: 0.0565

Gnomad EAS AF: 0.0965

Gnomad SAS AF: 0.0350

Gnomad FIN AF: 0.00245

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0123

Gnomad OTH AF: 0.0874

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

GnomAD4 genome AF: 0.0960 AC: 14608 AN: 152234 Hom.: 1771 Cov.: 33 AF XY: 0.0934 AC XY: 6951 AN XY: 74440

Gnomad4 AFR AF: 0.282

Gnomad4 AMR AF: 0.0626

Gnomad4 ASJ AF: 0.0565

Gnomad4 EAS AF: 0.0967

Gnomad4 SAS AF: 0.0350

Gnomad4 FIN AF: 0.00245

Gnomad4 NFE AF: 0.0123

Gnomad4 OTH AF: 0.0870

Alfa AF: 0.0614 Hom.: 152

Bravo AF: 0.109

Asia WGS AF: 0.0680 AC: 235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	3.4
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6092877; hg19: chr20-58712457;