Variant 15-90794393-ATT-AT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_000057.4(BLM):c.3210+44delT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 1,435,330 control chromosomes in the GnomAD database, including 21,695 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.17 ( 2314 hom., cov: 28)

Exomes 𝑓: 0.17 ( 19381 hom. )

Consequence

BLM
NM_000057.4 intron

Scores

Not classified

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.97

Variant links:

Genes affected

BLM (HGNC:1058): (BLM RecQ like helicase) The Bloom syndrome is an autosomal recessive disorder characterized by growth deficiency, microcephaly and immunodeficiency among others. It is caused by homozygous or compound heterozygous mutation in the gene encoding DNA helicase RecQ protein on chromosome 15q26. This Bloom-associated helicase unwinds a variety of DNA substrates including Holliday junction, and is involved in several pathways contributing to the maintenance of genome stability. Identification of pathogenic Bloom variants is required for heterozygote testing in at-risk families. [provided by RefSeq, May 2020]

BLM links:

BLM (HGNC:):

BLM links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 15-90794393-AT-A is Benign according to our data. Variant chr15-90794393-AT-A is described in ClinVar as [Likely_benign]. Clinvar id is 254779.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BLM	NM_000057.4 linkuse as main transcript	c.3210+44delT		intron_variant		ENST00000355112.8	NP_000048.1	P54132

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BLM	ENST00000355112.8 linkuse as main transcript	c.3210+44delT		intron_variant		1	NM_000057.4	ENSP00000347232.3		P54132

Frequencies

GnomAD3 genomes

AF:

0.172

AC:

26093

AN:

151742

Hom.:

2314

Cov.:

show subpopulations

Gnomad AFR

AF:

0.185

Gnomad AMI

AF:

0.0956

Gnomad AMR

AF:

0.117

Gnomad ASJ

AF:

0.171

Gnomad EAS

AF:

0.178

Gnomad SAS

AF:

0.0910

Gnomad FIN

AF:

0.146

Gnomad MID

AF:

0.156

Gnomad NFE

AF:

0.187

Gnomad OTH

AF:

0.161

GnomAD3 exomes

AF:

0.152

AC:

19006

AN:

124958

Hom.:

1553

AF XY:

0.149

AC XY:

10072

AN XY:

67528

show subpopulations

Gnomad AFR exome

AF:

0.183

Gnomad AMR exome

AF:

0.0984

Gnomad ASJ exome

AF:

0.163

Gnomad EAS exome

AF:

0.190

Gnomad SAS exome

AF:

0.0853

Gnomad FIN exome

AF:

0.145

Gnomad NFE exome

AF:

0.181

Gnomad OTH exome

AF:

0.158

GnomAD4 exome

AF:

0.169

AC:

216779

AN:

1283470

Hom.:

19381

Cov.:

AF XY:

0.167

AC XY:

106351

AN XY:

636028

show subpopulations

Gnomad4 AFR exome

AF:

0.179

Gnomad4 AMR exome

AF:

0.0987

Gnomad4 ASJ exome

AF:

0.163

Gnomad4 EAS exome

AF:

0.174

Gnomad4 SAS exome

AF:

0.0864

Gnomad4 FIN exome

AF:

0.145

Gnomad4 NFE exome

AF:

0.177

Gnomad4 OTH exome

AF:

0.164

GnomAD4 genome

AF:

0.172

AC:

26116

AN:

151860

Hom.:

2314

Cov.:

AF XY:

0.167

AC XY:

12399

AN XY:

74208

show subpopulations

Gnomad4 AFR

AF:

0.185

Gnomad4 AMR

AF:

0.117

Gnomad4 ASJ

AF:

0.171

Gnomad4 EAS

AF:

0.179

Gnomad4 SAS

AF:

0.0919

Gnomad4 FIN

AF:

0.146

Gnomad4 NFE

AF:

0.187

Gnomad4 OTH

AF:

0.161

Alfa

AF:

0.185

Hom.:

514

Bravo

AF:

0.170

Asia WGS

AF:

0.139

AC:

481

AN:

3460

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 03, 2015

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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