rs6027511

Positions:

• chr20-60323151-T-C

Variant summary

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

The ENST00000659856.1(MIR646HG):​n.353+142238T>C 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 0.183 in 152,026 control chromosomes in the GnomAD database, including 2,943 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 (2943 hom., cov: 31)
• Consequence: MIR646HG ENST00000659856.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.274 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.353+142238T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27764 AN: 151908 Hom.: 2927 Cov.: 31

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.00773

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.183 AC: 27836 AN: 152026 Hom.: 2943 Cov.: 31 AF XY: 0.177 AC XY: 13146 AN XY: 74290

Gnomad4 AFR AF: 0.279

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.00794

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.166

Gnomad4 OTH AF: 0.171

Alfa AF: 0.174 Hom.: 1142

Bravo AF: 0.188

Asia WGS AF: 0.115 AC: 402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.34
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6027511; hg19: chr20-58898209;