1-109294213-A-G

Variant summary

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

The NM_001010985.3(MYBPHL):c.*26T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 1,592,632 control chromosomes in the GnomAD database, including 80,189 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.27 (6412 hom., cov: 32)
  • Exomes 𝑓: 0.31 (73777 hom.)
• Consequence: MYBPHL NM_001010985.3 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.237

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 1-109294213-A-G is Benign according to our data. Variant chr1-109294213-A-G is described in ClinVar as [Benign]. Clinvar id is 1245843.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYBPHL	NM_001010985.3	c.*26T>C		3_prime_UTR_variant	8/9	ENST00000357155.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYBPHL	ENST00000357155.2	c.*26T>C		3_prime_UTR_variant	8/9	1	NM_001010985.3	P1
MYBPHL	ENST00000477962.1	n.373T>C		non_coding_transcript_exon_variant	3/4	1
MYBPHL	ENST00000489706.5	n.344T>C		non_coding_transcript_exon_variant	3/4	2

Frequencies

GnomAD3 genomes AF: 0.270 AC: 41035 AN: 152046 Hom.: 6410 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.294

GnomAD3 exomes AF: 0.329 AC: 82793 AN: 251286 Hom.: 14593 AF XY: 0.338 AC XY: 45855 AN XY: 135818

Gnomad AFR exome AF: 0.116

Gnomad AMR exome AF: 0.331

Gnomad ASJ exome AF: 0.380

Gnomad EAS exome AF: 0.461

Gnomad SAS exome AF: 0.441

Gnomad FIN exome AF: 0.354

Gnomad NFE exome AF: 0.300

Gnomad OTH exome AF: 0.323

GnomAD4 exome AF: 0.314 AC: 452668 AN: 1440468 Hom.: 73777 Cov.: 25 AF XY: 0.319 AC XY: 229024 AN XY: 718032

Gnomad4 AFR exome AF: 0.111

Gnomad4 AMR exome AF: 0.339

Gnomad4 ASJ exome AF: 0.378

Gnomad4 EAS exome AF: 0.478

Gnomad4 SAS exome AF: 0.438

Gnomad4 FIN exome AF: 0.346

Gnomad4 NFE exome AF: 0.300

Gnomad4 OTH exome AF: 0.320

GnomAD4 genome AF: 0.270 AC: 41041 AN: 152164 Hom.: 6412 Cov.: 32 AF XY: 0.279 AC XY: 20756 AN XY: 74382

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.392

Gnomad4 EAS AF: 0.471

Gnomad4 SAS AF: 0.453

Gnomad4 FIN AF: 0.360

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.293

Alfa AF: 0.293 Hom.: 3199

Bravo AF: 0.258

Asia WGS AF: 0.412 AC: 1435 AN: 3478

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

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	13
Dann	Benign	0.59

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.26		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.26		Position offset: 36

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

Publications

LitVar

Other links and lift over

dbSNP: rs3738777; hg19: chr1-109836835;