rs4728090

Variant summary

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

The ENST00000710955.1(ENSG00000292309):​n.306-15628C>T 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 0.508 in 152,154 control chromosomes in the GnomAD database, including 23,637 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 0.51 ( 23637 hom., cov: 33)

Consequence


ENST00000710955.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.178
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=-0.82).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000710955.1 linkuse as main transcriptn.306-15628C>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.509
AC:
77342
AN:
152036
Hom.:
23639
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.148
Gnomad AMI
AF:
0.779
Gnomad AMR
AF:
0.533
Gnomad ASJ
AF:
0.651
Gnomad EAS
AF:
0.699
Gnomad SAS
AF:
0.549
Gnomad FIN
AF:
0.614
Gnomad MID
AF:
0.621
Gnomad NFE
AF:
0.677
Gnomad OTH
AF:
0.552
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.508
AC:
77333
AN:
152154
Hom.:
23637
Cov.:
33
AF XY:
0.507
AC XY:
37694
AN XY:
74358
show subpopulations
Gnomad4 AFR
AF:
0.147
Gnomad4 AMR
AF:
0.533
Gnomad4 ASJ
AF:
0.651
Gnomad4 EAS
AF:
0.698
Gnomad4 SAS
AF:
0.550
Gnomad4 FIN
AF:
0.614
Gnomad4 NFE
AF:
0.677
Gnomad4 OTH
AF:
0.550
Alfa
AF:
0.650
Hom.:
61273
Bravo
AF:
0.488
Asia WGS
AF:
0.548
AC:
1908
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
4.5
DANN
Benign
0.61

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: rs4728090; hg19: chr7-127830114; API