Genetic Variant MYBPHL:c.731-74_731-72delAAA (chr1-109296441-ATTT-A) – ACMG Classification: Uncertain_significance (2 pts)

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001010985.3(MYBPHL):c.731-74_731-72delAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000745 in 1,246,930 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0 ( 0 hom., cov: 25)

Exomes 𝑓: 0.00075 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

MYBPHL
NM_001010985.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.471

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 Uncertain_significance. Variant got 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYBPHL	NM_001010985.3 link	c.731-74_731-72delAAA		intron_variant	Intron 5 of 8	ENST00000357155.2	NP_001010985.2	A2RUH7-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
MYBPHL	ENST00000357155.2 link	c.731-74_731-72delAAA	intron_variant	Intron 5 of 8	1	NM_001010985.3	ENSP00000349678.1	A2RUH7-1
MYBPHL	ENST00000477962.1 link	n.150-1147_150-1145delAAA	intron_variant	Intron 1 of 3	1
MYBPHL	ENST00000489706.5 link	n.-91_-89delAAA	upstream_gene_variant		2

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

141462

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.000745

AC:

929

AN:

1246930

Hom.:

AF XY:

0.000759

AC XY:

472

AN XY:

621614

show subpopulations

Gnomad4 AFR exome

AF:

0.00119

Gnomad4 AMR exome

AF:

0.000868

Gnomad4 ASJ exome

AF:

0.00112

Gnomad4 EAS exome

AF:

0.000948

Gnomad4 SAS exome

AF:

0.000802

Gnomad4 FIN exome

AF:

0.00125

Gnomad4 NFE exome

AF:

0.000674

Gnomad4 OTH exome

AF:

0.00104

GnomAD4 genome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

141462

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

68414

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

1-109296441-ATTTTT-ATT

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over