20-60224343-T-G

Position:

• chr20-60224343-T-G

Variant summary

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

The NR_046099.1(MIR646HG):​n.332+43430T>G 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 0.335 in 151,852 control chromosomes in the GnomAD database, including 9,829 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 0.34 (9829 hom., cov: 32)
• Consequence: MIR646HG NR_046099.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.933

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 (AFR) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR646HG	NR_046099.1	n.332+43430T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR646HG	ENST00000659856.1	n.353+43430T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50800 AN: 151734 Hom.: 9791 Cov.: 32

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.335 AC: 50910 AN: 151852 Hom.: 9829 Cov.: 32 AF XY: 0.337 AC XY: 24998 AN XY: 74220

Gnomad4 AFR AF: 0.540

Gnomad4 AMR AF: 0.309

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.260

Gnomad4 SAS AF: 0.259

Gnomad4 FIN AF: 0.344

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.303

Alfa AF: 0.253 Hom.: 6852

Bravo AF: 0.345

Asia WGS AF: 0.299 AC: 1042 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	4.3
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2865793; hg19: chr20-58799401;