GeneBe

rs7167936

Positions:

Variant summary

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

The ENST00000559909.1(MIR4713HG):​n.195-70635A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 152,094 control chromosomes in the GnomAD database, including 15,170 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 0.43 ( 15170 hom., cov: 32)

Consequence

MIR4713HG
ENST00000559909.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.47
Variant links:
Genes affected

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=-0.96).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MIR4713HGNR_146310.1 linkuse as main transcriptn.195-70635A>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MIR4713HGENST00000559909.1 linkuse as main transcriptn.195-70635A>G intron_variant 4

Frequencies

GnomAD3 genomes
AF:
0.430
AC:
65345
AN:
151976
Hom.:
15167
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.250
Gnomad AMI
AF:
0.523
Gnomad AMR
AF:
0.375
Gnomad ASJ
AF:
0.565
Gnomad EAS
AF:
0.498
Gnomad SAS
AF:
0.363
Gnomad FIN
AF:
0.523
Gnomad MID
AF:
0.418
Gnomad NFE
AF:
0.528
Gnomad OTH
AF:
0.452
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.430
AC:
65367
AN:
152094
Hom.:
15170
Cov.:
32
AF XY:
0.428
AC XY:
31787
AN XY:
74348
show subpopulations
Gnomad4 AFR
AF:
0.250
Gnomad4 AMR
AF:
0.374
Gnomad4 ASJ
AF:
0.565
Gnomad4 EAS
AF:
0.498
Gnomad4 SAS
AF:
0.365
Gnomad4 FIN
AF:
0.523
Gnomad4 NFE
AF:
0.528
Gnomad4 OTH
AF:
0.450
Alfa
AF:
0.481
Hom.:
2788
Bravo
AF:
0.415
Asia WGS
AF:
0.380
AC:
1322
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
0.13
DANN
Benign
0.42

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.

Other links and lift over

dbSNP: rs7167936; hg19: chr15-51499545; API