Variant 20-60487044-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.195 in 152,076 control chromosomes in the GnomAD database, including 3,088 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 0.19 ( 3088 hom., cov: 33)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.665

Variant links:

Genes affected

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.60487044A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
MIR646HG	ENST00000437035.5 linkuse as main transcript	n.428-40343A>G	intron_variant	5
MIR646HG	ENST00000659856.1 linkuse as main transcript	n.354-40343A>G	intron_variant
MIR646HG	ENST00000665114.1 linkuse as main transcript	n.359-40343A>G	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.195

AC:

29602

AN:

151958

Hom.:

3086

Cov.:

show subpopulations

Gnomad AFR

AF:

0.134

Gnomad AMI

AF:

0.217

Gnomad AMR

AF:

0.140

Gnomad ASJ

AF:

0.188

Gnomad EAS

AF:

0.135

Gnomad SAS

AF:

0.170

Gnomad FIN

AF:

0.260

Gnomad MID

AF:

0.247

Gnomad NFE

AF:

0.240

Gnomad OTH

AF:

0.205

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

GnomAD4 genome

AF:

0.195

AC:

29604

AN:

152076

Hom.:

3088

Cov.:

AF XY:

0.192

AC XY:

14275

AN XY:

74326

show subpopulations

Gnomad4 AFR

AF:

0.134

Gnomad4 AMR

AF:

0.140

Gnomad4 ASJ

AF:

0.188

Gnomad4 EAS

AF:

0.135

Gnomad4 SAS

AF:

0.170

Gnomad4 FIN

AF:

0.260

Gnomad4 NFE

AF:

0.240

Gnomad4 OTH

AF:

0.203

Alfa

AF:

0.223

Hom.:

5348

Bravo

AF:

0.181

Asia WGS

AF:

0.154

AC:

535

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.36

DANN

Benign

0.67

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over