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GeneBe

1-109296811-A-G

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_001010985.3(MYBPHL):c.702T>C(p.Thr234=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.987 in 1,614,102 control chromosomes in the GnomAD database, including 788,713 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.93 ( 67126 hom., cov: 31)
Exomes 𝑓: 0.99 ( 721587 hom. )

Consequence

MYBPHL
NM_001010985.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.813
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 1-109296811-A-G is Benign according to our data. Variant chr1-109296811-A-G is described in ClinVar as [Benign]. Clinvar id is 1265643.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.813 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.992 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MYBPHLNM_001010985.3 linkuse as main transcriptc.702T>C p.Thr234= synonymous_variant 5/9 ENST00000357155.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MYBPHLENST00000357155.2 linkuse as main transcriptc.702T>C p.Thr234= synonymous_variant 5/91 NM_001010985.3 P1A2RUH7-1
MYBPHLENST00000477962.1 linkuse as main transcriptn.150-1514T>C intron_variant, non_coding_transcript_variant 1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.934
AC:
142064
AN:
152090
Hom.:
67089
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.772
Gnomad AMI
AF:
1.00
Gnomad AMR
AF:
0.975
Gnomad ASJ
AF:
0.998
Gnomad EAS
AF:
1.00
Gnomad SAS
AF:
0.999
Gnomad FIN
AF:
1.00
Gnomad MID
AF:
0.984
Gnomad NFE
AF:
0.999
Gnomad OTH
AF:
0.954
GnomAD3 exomes
AF:
0.982
AC:
246979
AN:
251482
Hom.:
121715
AF XY:
0.987
AC XY:
134112
AN XY:
135914
show subpopulations
Gnomad AFR exome
AF:
0.759
Gnomad AMR exome
AF:
0.990
Gnomad ASJ exome
AF:
0.996
Gnomad EAS exome
AF:
1.00
Gnomad SAS exome
AF:
1.00
Gnomad FIN exome
AF:
1.00
Gnomad NFE exome
AF:
0.999
Gnomad OTH exome
AF:
0.990
GnomAD4 exome
AF:
0.993
AC:
1451548
AN:
1461894
Hom.:
721587
Cov.:
67
AF XY:
0.994
AC XY:
722753
AN XY:
727248
show subpopulations
Gnomad4 AFR exome
AF:
0.765
Gnomad4 AMR exome
AF:
0.988
Gnomad4 ASJ exome
AF:
0.995
Gnomad4 EAS exome
AF:
1.00
Gnomad4 SAS exome
AF:
1.00
Gnomad4 FIN exome
AF:
1.00
Gnomad4 NFE exome
AF:
0.999
Gnomad4 OTH exome
AF:
0.985
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.934
AC:
142161
AN:
152208
Hom.:
67126
Cov.:
31
AF XY:
0.936
AC XY:
69648
AN XY:
74422
show subpopulations
Gnomad4 AFR
AF:
0.772
Gnomad4 AMR
AF:
0.975
Gnomad4 ASJ
AF:
0.998
Gnomad4 EAS
AF:
1.00
Gnomad4 SAS
AF:
0.999
Gnomad4 FIN
AF:
1.00
Gnomad4 NFE
AF:
0.999
Gnomad4 OTH
AF:
0.955
Alfa
AF:
0.969
Hom.:
38527
Bravo
AF:
0.926
Asia WGS
AF:
0.986
AC:
3430
AN:
3478
EpiCase
AF:
0.999
EpiControl
AF:
0.998

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 submitterclinical testingGeneDxMay 04, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
Cadd
Benign
0.75
Dann
Benign
0.55

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.

Other links and lift over

dbSNP: rs1278285; hg19: chr1-109839433; API