chr20-60371431-C-A

Position:

• chr20-60371431-C-A

Variant summary

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

The ENST00000659856.1(MIR646HG):​n.354-155956C>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 0.306 in 152,082 control chromosomes in the GnomAD database, including 7,649 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 0.31 (7649 hom., cov: 33)
• Consequence: MIR646HG ENST00000659856.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR646HG	ENST00000659856.1	n.354-155956C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46487 AN: 151964 Hom.: 7651 Cov.: 33

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.306 AC: 46498 AN: 152082 Hom.: 7649 Cov.: 33 AF XY: 0.305 AC XY: 22668 AN XY: 74322

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.258

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.371

Gnomad4 OTH AF: 0.311

Alfa AF: 0.337 Hom.: 1930

Bravo AF: 0.290

Asia WGS AF: 0.208 AC: 728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.57
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs55681231; hg19: chr20-58946489;