dbSNP rs6574988: HISLA:n.329-2851T>C (chr14-88093648-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -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

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.418

Publications

12 publications found

Variant links:

COSMIC-nc: COSV73628071

Genes affected

HISLA (HGNC:49467): (HIF1A stabilizing long noncoding RNA)

HISLA links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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	Effect	Exon rank	TSL
HISLA	ENST00000553929.5 link	n.329-2851T>C	intron_variant	Intron 3 of 3	3
HISLA	ENST00000556673.2 link	n.62-2851T>C	intron_variant	Intron 1 of 1	3
HISLA	ENST00000653288.1 link	n.505-2851T>C	intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.912

AC:

138721

AN:

152036

Hom.:

63341

Cov.:

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.:

AF XY:

0.915

AC XY:

68054

AN XY:

74370

show subpopulations

African (AFR)

AF:

0.890

AC:

36945

AN:

41526

American (AMR)

AF:

0.939

AC:

14327

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.909

AC:

3154

AN:

3470

East Asian (EAS)

AF:

0.999

AC:

5156

AN:

5162

South Asian (SAS)

AF:

0.945

AC:

4554

AN:

4820

European-Finnish (FIN)

AF:

0.914

AC:

9701

AN:

10612

Middle Eastern (MID)

AF:

0.878

AC:

258

AN:

294

European-Non Finnish (NFE)

AF:

0.912

AC:

61984

AN:

67980

Other (OTH)

AF:

0.909

AC:

1921

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

632

1265

1897

2530

3162

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

910

1820

2730

3640

4550

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.912

Hom.:

180718

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

(source)

DANN

Benign

0.25

PhyloP100

0.42

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over