rs6574988

Variant summary

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

The ENST00000553929.5(HISLA):​n.329-2851T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.912 in 152,154 control chromosomes in the GnomAD database, including 63,398 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 0.91 ( 63398 hom., cov: 32)

Consequence

HISLA
ENST00000553929.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.418
Variant links:
Genes affected
HISLA (HGNC:49467): (HIF1A stabilizing long noncoding RNA)

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=-1.0).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
HISLAENST00000553929.5 linkn.329-2851T>C intron_variant Intron 3 of 3 3
HISLAENST00000556673.2 linkn.62-2851T>C intron_variant Intron 1 of 1 3
HISLAENST00000653288.1 linkn.505-2851T>C intron_variant Intron 3 of 3

Frequencies

GnomAD3 genomes
AF:
0.912
AC:
138721
AN:
152036
Hom.:
63341
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.890
Gnomad AMI
AF:
0.919
Gnomad AMR
AF:
0.938
Gnomad ASJ
AF:
0.909
Gnomad EAS
AF:
0.999
Gnomad SAS
AF:
0.945
Gnomad FIN
AF:
0.914
Gnomad MID
AF:
0.861
Gnomad NFE
AF:
0.912
Gnomad OTH
AF:
0.908
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.912
AC:
138838
AN:
152154
Hom.:
63398
Cov.:
32
AF XY:
0.915
AC XY:
68054
AN XY:
74370
show subpopulations
Gnomad4 AFR
AF:
0.890
Gnomad4 AMR
AF:
0.939
Gnomad4 ASJ
AF:
0.909
Gnomad4 EAS
AF:
0.999
Gnomad4 SAS
AF:
0.945
Gnomad4 FIN
AF:
0.914
Gnomad4 NFE
AF:
0.912
Gnomad4 OTH
AF:
0.909
Alfa
AF:
0.913
Hom.:
114595
Bravo
AF:
0.913
Asia WGS
AF:
0.975
AC:
3391
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
5.1
DANN
Benign
0.25

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: rs6574988; hg19: chr14-88559992; COSMIC: COSV73628071; API