Variant chr1-9151409-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The NR_132742.1(MIR34AHG):n.759G>A 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 0.0342 in 340,962 control chromosomes in the GnomAD database, including 274 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 0.033 ( 109 hom., cov: 32)

Exomes 𝑓: 0.035 ( 165 hom. )

Consequence

MIR34AHG
NR_132742.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.351

Variant links:

Genes affected

MIR34AHG (HGNC:51913): (MIR34A host gene)

MIR34AHG links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0331 (5039/152322) while in subpopulation NFE AF= 0.0483 (3288/68022). AF 95% confidence interval is 0.047. There are 109 homozygotes in gnomad4. There are 2411 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 109 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR34AHG	NR_132742.1 linkuse as main transcript	n.759G>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR34AHG	ENST00000635687.1 linkuse as main transcript	n.813G>A		non_coding_transcript_exon_variant	2/2	1

Frequencies

GnomAD3 genomes

AF:

0.0331

AC:

5042

AN:

152204

Hom.:

109

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00924

Gnomad AMI

AF:

0.0505

Gnomad AMR

AF:

0.0453

Gnomad ASJ

AF:

0.0297

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0108

Gnomad FIN

AF:

0.0351

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.0483

Gnomad OTH

AF:

0.0416

GnomAD4 exome

AF:

0.0351

AC:

6626

AN:

188640

Hom.:

165

Cov.:

AF XY:

0.0322

AC XY:

3347

AN XY:

103954

show subpopulations

Gnomad4 AFR exome

AF:

0.00782

Gnomad4 AMR exome

AF:

0.0397

Gnomad4 ASJ exome

AF:

0.0286

Gnomad4 EAS exome

AF:

0.000275

Gnomad4 SAS exome

AF:

0.0120

Gnomad4 FIN exome

AF:

0.0398

Gnomad4 NFE exome

AF:

0.0460

Gnomad4 OTH exome

AF:

0.0352

GnomAD4 genome

AF:

0.0331

AC:

5039

AN:

152322

Hom.:

109

Cov.:

AF XY:

0.0324

AC XY:

2411

AN XY:

74498

show subpopulations

Gnomad4 AFR

AF:

0.00921

Gnomad4 AMR

AF:

0.0452

Gnomad4 ASJ

AF:

0.0297

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0110

Gnomad4 FIN

AF:

0.0351

Gnomad4 NFE

AF:

0.0483

Gnomad4 OTH

AF:

0.0407

Alfa

AF:

0.0435

Hom.:

Bravo

AF:

0.0331

Asia WGS

AF:

0.00982

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

3.1

DANN

Benign

0.51

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