Variant 8-18085214-CTTT-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The ENST00000521775.6(ASAH1-AS1):n.809_811delTTT variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0501 in 236,212 control chromosomes in the GnomAD database, including 615 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.053 ( 368 hom., cov: 32)

Exomes 𝑓: 0.046 ( 247 hom. )

Consequence

ASAH1-AS1
ENST00000521775.6 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.707

Variant links:

Genes affected

ASAH1-AS1 (HGNC:):

ASAH1-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 8-18085214-CTTT-C is Benign according to our data. Variant chr8-18085214-CTTT-C is described in ClinVar as [Benign]. Clinvar id is 1225771.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ASAH1-AS1	NR_125429.1 linkuse as main transcript	n.73-23_73-21delTTT		intron_variant
ASAH1-AS1	NR_125430.1 linkuse as main transcript	n.72+280_72+282delTTT		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
ASAH1-AS1	ENST00000517798.2 linkuse as main transcript	n.834_836delTTT	non_coding_transcript_exon_variant	1/4	5
ASAH1-AS1	ENST00000521775.6 linkuse as main transcript	n.809_811delTTT	non_coding_transcript_exon_variant	1/3	4
ASAH1-AS1	ENST00000702451.1 linkuse as main transcript	n.836_838delTTT	non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.0524

AC:

7916

AN:

151004

Hom.:

366

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0839

Gnomad AMI

AF:

0.0242

Gnomad AMR

AF:

0.0912

Gnomad ASJ

AF:

0.0170

Gnomad EAS

AF:

0.178

Gnomad SAS

AF:

0.133

Gnomad FIN

AF:

0.00900

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.0183

Gnomad OTH

AF:

0.0502

GnomAD4 exome

AF:

0.0458

AC:

3898

AN:

85108

Hom.:

247

AF XY:

0.0531

AC XY:

2392

AN XY:

45074

show subpopulations

Gnomad4 AFR exome

AF:

0.0745

Gnomad4 AMR exome

AF:

0.0803

Gnomad4 ASJ exome

AF:

0.0195

Gnomad4 EAS exome

AF:

0.166

Gnomad4 SAS exome

AF:

0.107

Gnomad4 FIN exome

AF:

0.0131

Gnomad4 NFE exome

AF:

0.0179

Gnomad4 OTH exome

AF:

0.0356

GnomAD4 genome

AF:

0.0525

AC:

7939

AN:

151104

Hom.:

368

Cov.:

AF XY:

0.0556

AC XY:

4099

AN XY:

73766

show subpopulations

Gnomad4 AFR

AF:

0.0841

Gnomad4 AMR

AF:

0.0912

Gnomad4 ASJ

AF:

0.0170

Gnomad4 EAS

AF:

0.179

Gnomad4 SAS

AF:

0.133

Gnomad4 FIN

AF:

0.00900

Gnomad4 NFE

AF:

0.0183

Gnomad4 OTH

AF:

0.0501

Alfa

AF:

0.0336

Hom.:

Bravo

AF:

0.0563

Asia WGS

AF:

0.153

AC:

532

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 10, 2019

- -

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over