Variant chr10-86756209-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000608826.1(ENSG00000272631):n.90C>T 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 0.289 in 151,980 control chromosomes in the GnomAD database, including 7,637 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.29 ( 7630 hom., cov: 32)

Exomes 𝑓: 0.70 ( 7 hom. )

Consequence

ENST00000608826.1 non_coding_transcript_exon

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.0600

Variant links:

Genes affected

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.63).

BP6

Variant 10-86756209-G-A is Benign according to our data. Variant chr10-86756209-G-A is described in ClinVar as [Benign]. Clinvar id is 1229698.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86756209-G-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Protein
BMPR1A	NM_001406562.1 linkuse as main transcript	c.-373+105G>A	intron_variant	NP_001393491.1
BMPR1A	NM_001406564.1 linkuse as main transcript	c.-373+246G>A	intron_variant	NP_001393493.1
BMPR1A	NM_001406566.1 linkuse as main transcript	c.-268+246G>A	intron_variant	NP_001393495.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000608826.1 linkuse as main transcript	n.90C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.289

AC:

43948

AN:

151834

Hom.:

7629

Cov.:

show subpopulations

Gnomad AFR

AF:

0.123

Gnomad AMI

AF:

0.163

Gnomad AMR

AF:

0.324

Gnomad ASJ

AF:

0.397

Gnomad EAS

AF:

0.694

Gnomad SAS

AF:

0.352

Gnomad FIN

AF:

0.391

Gnomad MID

AF:

0.322

Gnomad NFE

AF:

0.328

Gnomad OTH

AF:

0.294

GnomAD4 exome

AF:

0.700

AC:

AN:

Hom.:

Cov.:

AF XY:

0.750

AC XY:

AN XY:

show subpopulations

Gnomad4 AMR exome

AF:

0.500

Gnomad4 EAS exome

AF:

1.00

Gnomad4 SAS exome

AF:

0.500

Gnomad4 NFE exome

AF:

0.708

GnomAD4 genome

AF:

0.289

AC:

43955

AN:

151950

Hom.:

7630

Cov.:

AF XY:

0.296

AC XY:

21997

AN XY:

74286

show subpopulations

Gnomad4 AFR

AF:

0.123

Gnomad4 AMR

AF:

0.324

Gnomad4 ASJ

AF:

0.397

Gnomad4 EAS

AF:

0.695

Gnomad4 SAS

AF:

0.353

Gnomad4 FIN

AF:

0.391

Gnomad4 NFE

AF:

0.328

Gnomad4 OTH

AF:

0.292

Alfa

AF:

0.313

Hom.:

1376

Bravo

AF:

0.278

Asia WGS

AF:

0.433

AC:

1502

AN:

3470

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 14, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.63

CADD

Benign

6.4

DANN

Benign

0.84

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