Variant 16-2271814-GC-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The ENST00000562838.1(MIR3677HG):n.325delC 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 0.00000268 in 373,276 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0000027 ( 0 hom. )

Consequence

MIR3677HG
ENST00000562838.1 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.471

Variant links:

Genes affected

MIR940 (HGNC:):

MIR940 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
MIR940	NR_030636.1 linkuse as main transcript	n.73delC	non_coding_transcript_exon_variant	1/1
MIR3677HG	NR_132988.1 linkuse as main transcript	n.325delC	non_coding_transcript_exon_variant	2/3
MIR940	unassigned_transcript_2778 use as main transcript	n.14delC	non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
MIR940	ENST00000401276.3 linkuse as main transcript	n.73delC	non_coding_transcript_exon_variant	1/1	6
MIR3677HG	ENST00000562838.1 linkuse as main transcript	n.325delC	non_coding_transcript_exon_variant	2/3	2
MIR3677HG	ENST00000563734.1 linkuse as main transcript	n.112-1168delC	intron_variant		3
MIR3677HG	ENST00000567888.1 linkuse as main transcript	n.222-1168delC	intron_variant		5

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000268

AC:

AN:

373276

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

213310

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.0000287

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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