1-109296441-AT-A

Position:

• chr1-109296441-AT-A

Variant summary

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

The NM_001010985.3(MYBPHL):​c.731-72del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 141,140 control chromosomes in the GnomAD database, including 931 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.11 (931 hom., cov: 25)
  • Exomes 𝑓: 0.33 (238 hom.)
  • Failed GnomAD Quality Control
• 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-AT-A is Benign according to our data. Variant chr1-109296441-AT-A is described in ClinVar as [Benign]. Clinvar id is 1268940.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYBPHL	NM_001010985.3	c.731-72del		intron_variant		ENST00000357155.2	NP_001010985.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYBPHL	ENST00000357155.2	c.731-72del		intron_variant		1	NM_001010985.3	ENSP00000349678	P1
MYBPHL	ENST00000477962.1	n.150-1145del		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.111 AC: 15596 AN: 141102 Hom.: 926 Cov.: 25

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.0648

Gnomad ASJ AF: 0.0248

Gnomad EAS AF: 0.0339

Gnomad SAS AF: 0.0330

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.0362

Gnomad NFE AF: 0.0925

Gnomad OTH AF: 0.0815

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.326 AC: 376905 AN: 1156304 Hom.: 238 AF XY: 0.329 AC XY: 188895 AN XY: 574950

Gnomad4 AFR exome AF: 0.352

Gnomad4 AMR exome AF: 0.345

Gnomad4 ASJ exome AF: 0.327

Gnomad4 EAS exome AF: 0.368

Gnomad4 SAS exome AF: 0.344

Gnomad4 FIN exome AF: 0.337

Gnomad4 NFE exome AF: 0.321

Gnomad4 OTH exome AF: 0.334

GnomAD4 genome AF: 0.111 AC: 15626 AN: 141140 Hom.: 931 Cov.: 25 AF XY: 0.110 AC XY: 7496 AN XY: 68302

Gnomad4 AFR AF: 0.184

Gnomad4 AMR AF: 0.0647

Gnomad4 ASJ AF: 0.0248

Gnomad4 EAS AF: 0.0332

Gnomad4 SAS AF: 0.0327

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.0925

Gnomad4 OTH AF: 0.0810

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;