20-60239370-T-C

Variant names:

• chr20-60239370-T-C
• rs1535028
• ENST00000421257.1:n.35+58457T>C

Variant summary

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

The ENST00000432910.5(MIR646HG):​n.332+58457T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 152,150 control chromosomes in the GnomAD database, including 20,673 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 0.46 (20673 hom., cov: 33)
• Consequence: MIR646HG ENST00000432910.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.83 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR646HG	NR_046099.1	n.332+58457T>C		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR646HG	ENST00000421257.1	n.35+58457T>C		intron_variant	Intron 1 of 2	3
MIR646HG	ENST00000427820.1	n.27-7423T>C		intron_variant	Intron 1 of 3	5
MIR646HG	ENST00000431181.5	n.767-6668T>C		intron_variant	Intron 7 of 7	3

Frequencies

GnomAD3 genomes AF: 0.464 AC: 70561 AN: 152032 Hom.: 20609 Cov.: 33

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.404

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.465 AC: 70691 AN: 152150 Hom.: 20673 Cov.: 33 AF XY: 0.466 AC XY: 34638 AN XY: 74388

Gnomad4 AFR AF: 0.838

Gnomad4 AMR AF: 0.379

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.297

Gnomad4 OTH AF: 0.423

Alfa AF: 0.339 Hom.: 5979

Bravo AF: 0.478

Asia WGS AF: 0.350 AC: 1219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.062
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1535028; hg19: chr20-58814428;