NM_001010985.3:c.731-73_731-72dupAA

Variant names:

• chr1-109296441-A-ATT
• rs59806839
• NM_001010985.3:c.731-73_731-72dupAA

Variant summary

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

The NM_001010985.3(MYBPHL):​c.731-73_731-72dupAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00154 in 1,390,388 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 0.00061 (0 hom., cov: 25)
  • Exomes 𝑓: 0.0016 (0 hom.)
• Consequence: MYBPHL NM_001010985.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.471

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]

ACMG classification

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	c.731-73_731-72dupAA		intron_variant	Intron 5 of 8	ENST00000357155.2	NP_001010985.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYBPHL	ENST00000357155.2	c.731-72_731-71insAA		intron_variant	Intron 5 of 8	1	NM_001010985.3	ENSP00000349678.1
MYBPHL	ENST00000477962.1	n.150-1145_150-1144insAA		intron_variant	Intron 1 of 3	1
MYBPHL	ENST00000489706.5	n.-89_-88insAA		upstream_gene_variant		2

Frequencies

GnomAD3 genomes AF: 0.000615 AC: 87 AN: 141480 Hom.: 0 Cov.: 25

Gnomad AFR AF: 0.00133

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000142

Gnomad ASJ AF: 0.000302

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000229

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000480

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00165 AC: 2056 AN: 1248870 Hom.: 0 AF XY: 0.00165 AC XY: 1025 AN XY: 622698

Gnomad4 AFR exome AF: 0.00260

Gnomad4 AMR exome AF: 0.000601

Gnomad4 ASJ exome AF: 0.00144

Gnomad4 EAS exome AF: 0.000400

Gnomad4 SAS exome AF: 0.00107

Gnomad4 FIN exome AF: 0.000875

Gnomad4 NFE exome AF: 0.00177

Gnomad4 OTH exome AF: 0.00169

GnomAD4 genome AF: 0.000615 AC: 87 AN: 141518 Hom.: 0 Cov.: 25 AF XY: 0.000438 AC XY: 30 AN XY: 68480

Gnomad4 AFR AF: 0.00132

Gnomad4 AMR AF: 0.000142

Gnomad4 ASJ AF: 0.000302

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000229

Gnomad4 NFE AF: 0.000480

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs59806839; hg19: chr1-109839063;