rs6507763

Variant summary

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

The NR_147192.1(MIR4527HG):​n.39-44296G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,160 control chromosomes in the GnomAD database, including 2,650 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 0.18 ( 2650 hom., cov: 33)

Consequence

MIR4527HG
NR_147192.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.78
Variant links:
Genes affected
MIR4527HG (HGNC:31724): (MIR4527 host gene)

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=-0.78).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MIR4527HGNR_147192.1 linkuse as main transcriptn.39-44296G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000565127.1 linkuse as main transcriptn.276-15114G>A intron_variant, non_coding_transcript_variant 4
MIR4527HGENST00000586905.3 linkuse as main transcriptn.38-44296G>A intron_variant, non_coding_transcript_variant 1
MIR4527HGENST00000598649.1 linkuse as main transcriptn.74-31434G>A intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.181
AC:
27483
AN:
152042
Hom.:
2645
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.211
Gnomad AMI
AF:
0.271
Gnomad AMR
AF:
0.156
Gnomad ASJ
AF:
0.125
Gnomad EAS
AF:
0.108
Gnomad SAS
AF:
0.154
Gnomad FIN
AF:
0.270
Gnomad MID
AF:
0.101
Gnomad NFE
AF:
0.165
Gnomad OTH
AF:
0.153
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.181
AC:
27501
AN:
152160
Hom.:
2650
Cov.:
33
AF XY:
0.183
AC XY:
13619
AN XY:
74386
show subpopulations
Gnomad4 AFR
AF:
0.211
Gnomad4 AMR
AF:
0.156
Gnomad4 ASJ
AF:
0.125
Gnomad4 EAS
AF:
0.108
Gnomad4 SAS
AF:
0.154
Gnomad4 FIN
AF:
0.270
Gnomad4 NFE
AF:
0.165
Gnomad4 OTH
AF:
0.151
Alfa
AF:
0.168
Hom.:
1150
Bravo
AF:
0.171
Asia WGS
AF:
0.126
AC:
435
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.78
CADD
Benign
16
DANN
Benign
0.68

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: rs6507763; hg19: chr18-45056671; API