Variant rs12903401 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000711326.1(ENSG00000292375):n.352G>C 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 0.444 in 501,760 control chromosomes in the GnomAD database, including 52,598 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.41 ( 13946 hom., cov: 32)

Exomes 𝑓: 0.46 ( 38652 hom. )

Consequence

ENST00000711326.1 non_coding_transcript_exon

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.402

Variant links:

Genes affected

(HGNC:):

links:

ANKRD34C-AS1 (HGNC:48618): (ANKRD34C antisense RNA 1)

ANKRD34C-AS1 links:

MIR184 (HGNC:31555): (microRNA 184) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of target mRNAs. This microRNA represents the most abundant miRNA in the corneal and lens epithelia of the eye and has been shown to interfere with target binding by another miRNA, miR-205. Through regulation of the VEGF and Akt signaling pathways, this microRNA may inhibit corneal angiogenesis. Mutations in the seed region of this microRNA cause familial keratoconus with cataract, also known as EDICT syndrome. [provided by RefSeq, Mar 2017]

MIR184 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.68).

BP6

Variant 15-79209754-G-C is Benign according to our data. Variant chr15-79209754-G-C is described in ClinVar as [Benign]. Clinvar id is 1223338.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANKRD34C-AS1	NR_038997.1 linkuse as main transcript	n.298-17652C>G		intron_variant, non_coding_transcript_variant
MIR184	NR_029705.1 linkuse as main transcript			upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons
	ENST00000711326.1 linkuse as main transcript	n.352G>C	non_coding_transcript_exon_variant	1/2
ANKRD34C-AS1	ENST00000685737.1 linkuse as main transcript	n.316+73895C>G	intron_variant, non_coding_transcript_variant
MIR184	ENST00000384962.1 linkuse as main transcript		upstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.406

AC:

61592

AN:

151888

Hom.:

13937

Cov.:

show subpopulations

Gnomad AFR

AF:

0.197

Gnomad AMI

AF:

0.366

Gnomad AMR

AF:

0.526

Gnomad ASJ

AF:

0.489

Gnomad EAS

AF:

0.552

Gnomad SAS

AF:

0.364

Gnomad FIN

AF:

0.476

Gnomad MID

AF:

0.560

Gnomad NFE

AF:

0.481

Gnomad OTH

AF:

0.450

GnomAD3 exomes

AF:

0.464

AC:

115006

AN:

247820

Hom.:

27733

AF XY:

0.462

AC XY:

61934

AN XY:

134128

show subpopulations

Gnomad AFR exome

AF:

0.190

Gnomad AMR exome

AF:

0.542

Gnomad ASJ exome

AF:

0.507

Gnomad EAS exome

AF:

0.566

Gnomad SAS exome

AF:

0.358

Gnomad FIN exome

AF:

0.481

Gnomad NFE exome

AF:

0.483

Gnomad OTH exome

AF:

0.485

GnomAD4 exome

AF:

0.461

AC:

161409

AN:

349756

Hom.:

38652

Cov.:

AF XY:

0.453

AC XY:

89226

AN XY:

197054

show subpopulations

Gnomad4 AFR exome

AF:

0.199

Gnomad4 AMR exome

AF:

0.541

Gnomad4 ASJ exome

AF:

0.508

Gnomad4 EAS exome

AF:

0.570

Gnomad4 SAS exome

AF:

0.366

Gnomad4 FIN exome

AF:

0.480

Gnomad4 NFE exome

AF:

0.481

Gnomad4 OTH exome

AF:

0.463

GnomAD4 genome

AF:

0.405

AC:

61610

AN:

152004

Hom.:

13946

Cov.:

AF XY:

0.409

AC XY:

30358

AN XY:

74306

show subpopulations

Gnomad4 AFR

AF:

0.196

Gnomad4 AMR

AF:

0.527

Gnomad4 ASJ

AF:

0.489

Gnomad4 EAS

AF:

0.553

Gnomad4 SAS

AF:

0.364

Gnomad4 FIN

AF:

0.476

Gnomad4 NFE

AF:

0.481

Gnomad4 OTH

AF:

0.449

Alfa

AF:

0.445

Hom.:

2931

Bravo

AF:

0.408

Asia WGS

AF:

0.420

AC:

1463

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 09, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

6.3

DANN

Benign

0.84

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over