Genetic Variant MIR646HG:n.430A>T (chr20-60070651-A-T) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The ENST00000625080.1(MIR646HG):n.430A>T 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 0.00000411 in 1,215,574 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)

Exomes 𝑓: 0.0000041 ( 0 hom. )

Consequence

MIR646HG
ENST00000625080.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.637

Publications

0 publications found

Variant links:

Genes affected

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

MIR646HG links:

LINC02910 (HGNC:26601): (long intergenic non-protein coding RNA 2910)

LINC02910 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (REVEL=0.089).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LINC02910	NR_161291.1 link	n.430A>T	non_coding_transcript_exon_variant	Exon 4 of 4
LINC02910	NR_161292.1 link	n.350A>T	non_coding_transcript_exon_variant	Exon 3 of 3
LINC02910	NR_161293.1 link	n.376-337A>T	intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MIR646HG	ENST00000625080.1 link	n.430A>T	non_coding_transcript_exon_variant	Exon 4 of 4	2
MIR646HG	ENST00000660831.1 link	n.422A>T	non_coding_transcript_exon_variant	Exon 3 of 3
MIR646HG	ENST00000715828.1 link	n.82+14643A>T	intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000411

AC:

AN:

1215574

Hom.:

Cov.:

AF XY:

0.00000166

AC XY:

AN XY:

602444

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

26300

American (AMR)

AF:

0.00

AC:

AN:

37290

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

16896

East Asian (EAS)

AF:

0.00

AC:

AN:

16806

South Asian (SAS)

AF:

0.00

AC:

AN:

83226

European-Finnish (FIN)

AF:

0.00

AC:

AN:

32596

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4474

European-Non Finnish (NFE)

AF:

0.00000524

AC:

AN:

953960

Other (OTH)

AF:

0.00

AC:

AN:

44026

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.72

(source)

DANN

Benign

0.97

PhyloP100

-0.64

Splicing

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

Publications

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20-60070651-A-T

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over