1-109296441-A-AT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001010985.3(MYBPHL):c.731-72_731-71insA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0927 in 1,371,524 control chromosomes in the GnomAD database, including 413 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.070 (365 hom., cov: 25)
  • Exomes 𝑓: 0.095 (48 hom.)
• Consequence: MYBPHL NM_001010985.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• 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 Benign. Variant got -10 ACMG points.

• BP6: Variant 1-109296441-A-AT is Benign according to our data. Variant chr1-109296441-A-AT is described in ClinVar as [Benign]. Clinvar id is 1238412.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0773 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYBPHL	NM_001010985.3	c.731-72_731-71insA		intron_variant		ENST00000357155.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYBPHL	ENST00000357155.2	c.731-72_731-71insA		intron_variant		1	NM_001010985.3	P1
MYBPHL	ENST00000477962.1	n.150-1145_150-1144insA		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0704 AC: 9955 AN: 141450 Hom.: 365 Cov.: 25

Gnomad AFR AF: 0.0798

Gnomad AMI AF: 0.0916

Gnomad AMR AF: 0.0429

Gnomad ASJ AF: 0.0647

Gnomad EAS AF: 0.00330

Gnomad SAS AF: 0.0807

Gnomad FIN AF: 0.0470

Gnomad MID AF: 0.0691

Gnomad NFE AF: 0.0783

Gnomad OTH AF: 0.0691

GnomAD4 exome AF: 0.0953 AC: 117254 AN: 1230038 Hom.: 48 AF XY: 0.0934 AC XY: 57273 AN XY: 613406

Gnomad4 AFR exome AF: 0.0920

Gnomad4 AMR exome AF: 0.0520

Gnomad4 ASJ exome AF: 0.0837

Gnomad4 EAS exome AF: 0.0398

Gnomad4 SAS exome AF: 0.0765

Gnomad4 FIN exome AF: 0.0554

Gnomad4 NFE exome AF: 0.102

Gnomad4 OTH exome AF: 0.0892

GnomAD4 genome AF: 0.0703 AC: 9950 AN: 141486 Hom.: 365 Cov.: 25 AF XY: 0.0683 AC XY: 4675 AN XY: 68462

Gnomad4 AFR AF: 0.0796

Gnomad4 AMR AF: 0.0428

Gnomad4 ASJ AF: 0.0647

Gnomad4 EAS AF: 0.00331

Gnomad4 SAS AF: 0.0808

Gnomad4 FIN AF: 0.0470

Gnomad4 NFE AF: 0.0783

Gnomad4 OTH AF: 0.0687

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 13, 2021

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs59806839; hg19: chr1-109839063;