rs6027511

Variant names:

• chr20-60323151-T-C
• rs6027511
• ENST00000663127.1:n.865T>C

Variant summary

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

The ENST00000663127.1(MIR646HG):​n.865T>C variant causes a non coding transcript exon 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 ENST00000663127.1 non_coding_transcript_exon
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR646HG	ENST00000663127.1	n.865T>C		non_coding_transcript_exon_variant	Exon 2 of 2
MIR646HG	ENST00000421257.1	n.114-7722T>C		intron_variant	Intron 2 of 2	3
MIR646HG	ENST00000437035.5	n.427+2293T>C		intron_variant	Intron 4 of 4	5

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;