Variant chr1-109294213-A-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000357155.2(MYBPHL):c.*26T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 1,592,632 control chromosomes in the GnomAD database, including 80,189 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.27 ( 6412 hom., cov: 32)

Exomes 𝑓: 0.31 ( 73777 hom. )

Consequence

MYBPHL
ENST00000357155.2 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.237

Variant links:

Genes affected

MYBPHL (HGNC:30434): (myosin binding protein H like) This gene encodes a protein with two immunoglobulin superfamily domains and a fibronectin 3 domain. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2012]

MYBPHL links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 1-109294213-A-G is Benign according to our data. Variant chr1-109294213-A-G is described in ClinVar as [Benign]. Clinvar id is 1245843.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYBPHL	NM_001010985.3 linkuse as main transcript	c.*26T>C		3_prime_UTR_variant	8/9	ENST00000357155.2	NP_001010985.2

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYBPHL	ENST00000357155.2 linkuse as main transcript	c.*26T>C	3_prime_UTR_variant	8/9	1	NM_001010985.3	ENSP00000349678	P1	A2RUH7-1
MYBPHL	ENST00000477962.1 linkuse as main transcript	n.373T>C	non_coding_transcript_exon_variant	3/4	1
MYBPHL	ENST00000489706.5 linkuse as main transcript	n.344T>C	non_coding_transcript_exon_variant	3/4	2

Frequencies

GnomAD3 genomes

AF:

0.270

AC:

41035

AN:

152046

Hom.:

6410

Cov.:

show subpopulations

Gnomad AFR

AF:

0.119

Gnomad AMI

AF:

0.353

Gnomad AMR

AF:

0.328

Gnomad ASJ

AF:

0.392

Gnomad EAS

AF:

0.471

Gnomad SAS

AF:

0.454

Gnomad FIN

AF:

0.360

Gnomad MID

AF:

0.307

Gnomad NFE

AF:

0.298

Gnomad OTH

AF:

0.294

GnomAD3 exomes

AF:

0.329

AC:

82793

AN:

251286

Hom.:

14593

AF XY:

0.338

AC XY:

45855

AN XY:

135818

show subpopulations

Gnomad AFR exome

AF:

0.116

Gnomad AMR exome

AF:

0.331

Gnomad ASJ exome

AF:

0.380

Gnomad EAS exome

AF:

0.461

Gnomad SAS exome

AF:

0.441

Gnomad FIN exome

AF:

0.354

Gnomad NFE exome

AF:

0.300

Gnomad OTH exome

AF:

0.323

GnomAD4 exome

AF:

0.314

AC:

452668

AN:

1440468

Hom.:

73777

Cov.:

AF XY:

0.319

AC XY:

229024

AN XY:

718032

show subpopulations

Gnomad4 AFR exome

AF:

0.111

Gnomad4 AMR exome

AF:

0.339

Gnomad4 ASJ exome

AF:

0.378

Gnomad4 EAS exome

AF:

0.478

Gnomad4 SAS exome

AF:

0.438

Gnomad4 FIN exome

AF:

0.346

Gnomad4 NFE exome

AF:

0.300

Gnomad4 OTH exome

AF:

0.320

GnomAD4 genome

AF:

0.270

AC:

41041

AN:

152164

Hom.:

6412

Cov.:

AF XY:

0.279

AC XY:

20756

AN XY:

74382

show subpopulations

Gnomad4 AFR

AF:

0.119

Gnomad4 AMR

AF:

0.328

Gnomad4 ASJ

AF:

0.392

Gnomad4 EAS

AF:

0.471

Gnomad4 SAS

AF:

0.453

Gnomad4 FIN

AF:

0.360

Gnomad4 NFE

AF:

0.298

Gnomad4 OTH

AF:

0.293

Alfa

AF:

0.293

Hom.:

3199

Bravo

AF:

0.258

Asia WGS

AF:

0.412

AC:

1435

AN:

3478

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	May 13, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

DANN

Benign

0.59

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.26

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.26

Position offset: 36

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