ENST00000663127.1:n.865T>C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

Genes affected

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

ENSG00000309272 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000663127.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR646HG	ENST00000663127.1		n.865T>C		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000309272	ENST00000839994.1		n.461A>G		non_coding_transcript_exon	Exon 2 of 2
	MIR646HG	ENST00000421257.1	TSL:3	n.114-7722T>C		intron	N/A

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

African (AFR) AF: 0.279 AC: 11558 AN: 41464

American (AMR) AF: 0.114 AC: 1738 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 497 AN: 3472

East Asian (EAS) AF: 0.00794 AC: 41 AN: 5164

South Asian (SAS) AF: 0.204 AC: 979 AN: 4808

European-Finnish (FIN) AF: 0.116 AC: 1230 AN: 10568

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11298 AN: 67960

Other (OTH) AF: 0.171 AC: 359 AN: 2102

Alfa AF: 0.186 Hom.: 2726

Bravo AF: 0.188

Asia WGS AF: 0.115 AC: 402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.34
DANN	Benign	0.60
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs6027511; hg19: chr20-58898209;