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GeneBe

rs11398689

chr16-85933613-T-TG

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000646214.1(ENSG00000285163):n.77+8556dup 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 0.719 in 145,890 control chromosomes in the GnomAD database, including 38,608 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.72 ( 38608 hom., cov: 0)

Consequence


ENST00000646214.1 intron, non_coding_transcript

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.902
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.888 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
ENST00000646214.1 linkuse as main transcriptn.77+8556dup intron_variant, non_coding_transcript_variant
ENST00000645383.1 linkuse as main transcriptn.393+1342dup intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.719
AC:
104792
AN:
145810
Hom.:
38557
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.895
Gnomad AMI
AF:
0.680
Gnomad AMR
AF:
0.703
Gnomad ASJ
AF:
0.567
Gnomad EAS
AF:
0.760
Gnomad SAS
AF:
0.667
Gnomad FIN
AF:
0.724
Gnomad MID
AF:
0.517
Gnomad NFE
AF:
0.629
Gnomad OTH
AF:
0.657
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.719
AC:
104890
AN:
145890
Hom.:
38608
Cov.:
0
AF XY:
0.721
AC XY:
50754
AN XY:
70346
show subpopulations
Gnomad4 AFR
AF:
0.895
Gnomad4 AMR
AF:
0.704
Gnomad4 ASJ
AF:
0.567
Gnomad4 EAS
AF:
0.761
Gnomad4 SAS
AF:
0.667
Gnomad4 FIN
AF:
0.724
Gnomad4 NFE
AF:
0.629
Gnomad4 OTH
AF:
0.659
Alfa
AF:
0.482
Hom.:
1077
Asia WGS
AF:
0.721
AC:
2496
AN:
3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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: rs11398689; hg19: chr16-85967219; API