Variant chr11-93733700-G-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NR_031639.1(MIR1304):n.65C>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 0.951 in 438,510 control chromosomes in the GnomAD database, including 200,248 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 0.90 ( 61277 hom., cov: 21)

Exomes 𝑓: 0.98 ( 138971 hom. )

Consequence

MIR1304
NR_031639.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.165

Variant links:

Genes affected

MIR1304 (HGNC:35302): (microRNA 1304) 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 mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

MIR1304 links:

TAF1D (HGNC:28759): (TATA-box binding protein associated factor, RNA polymerase I subunit D) TAF1D is a member of the SL1 complex, which includes TBP (MIM 600075) and TAF1A (MIM 604903), TAF1B (MIM 604904), and TAF1C (MIM 604905), and plays a role in RNA polymerase I transcription (Wang et al., 2004 [PubMed 15520167]; Gorski et al., 2007 [PubMed 17318177]).[supplied by OMIM, Jun 2009]

TAF1D 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=-0.8).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.984 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
MIR1304	NR_031639.1 linkuse as main transcript	n.65C>A	non_coding_transcript_exon_variant	1/1
TAF1D	NR_146090.2 linkuse as main transcript	n.1095-195C>A	intron_variant, non_coding_transcript_variant
TAF1D	NR_146091.2 linkuse as main transcript	n.1095-303C>A	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR1304	ENST00000408243.1 linkuse as main transcript	n.65C>A		mature_miRNA_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.902

AC:

133202

AN:

147622

Hom.:

61253

Cov.:

show subpopulations

Gnomad AFR

AF:

0.696

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

0.934

Gnomad ASJ

AF:

0.971

Gnomad EAS

AF:

0.944

Gnomad SAS

AF:

0.989

Gnomad FIN

AF:

0.999

Gnomad MID

AF:

0.911

Gnomad NFE

AF:

0.990

Gnomad OTH

AF:

0.899

GnomAD3 exomes

AF:

0.958

AC:

161647

AN:

168728

Hom.:

77964

AF XY:

0.964

AC XY:

88731

AN XY:

92042

show subpopulations

Gnomad AFR exome

AF:

0.687

Gnomad AMR exome

AF:

0.970

Gnomad ASJ exome

AF:

0.971

Gnomad EAS exome

AF:

0.939

Gnomad SAS exome

AF:

0.984

Gnomad FIN exome

AF:

1.00

Gnomad NFE exome

AF:

0.990

Gnomad OTH exome

AF:

0.961

GnomAD4 exome

AF:

0.976

AC:

283887

AN:

290766

Hom.:

138971

Cov.:

AF XY:

0.979

AC XY:

162026

AN XY:

165576

show subpopulations

Gnomad4 AFR exome

AF:

0.692

Gnomad4 AMR exome

AF:

0.970

Gnomad4 ASJ exome

AF:

0.970

Gnomad4 EAS exome

AF:

0.938

Gnomad4 SAS exome

AF:

0.986

Gnomad4 FIN exome

AF:

0.999

Gnomad4 NFE exome

AF:

0.991

Gnomad4 OTH exome

AF:

0.967

GnomAD4 genome

AF:

0.902

AC:

133280

AN:

147744

Hom.:

61277

Cov.:

AF XY:

0.904

AC XY:

65317

AN XY:

72246

show subpopulations

Gnomad4 AFR

AF:

0.696

Gnomad4 AMR

AF:

0.934

Gnomad4 ASJ

AF:

0.971

Gnomad4 EAS

AF:

0.944

Gnomad4 SAS

AF:

0.990

Gnomad4 FIN

AF:

0.999

Gnomad4 NFE

AF:

0.990

Gnomad4 OTH

AF:

0.900

Alfa

AF:

0.960

Hom.:

7517

Bravo

AF:

0.886

Asia WGS

AF:

0.950

AC:

3305

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

2.9

DANN

Benign

0.86

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