XM_047421205.1:c.112+14G>C

Variant names:

• chr1-203177038-C-G
• rs883125
• XM_047421205.1:c.112+14G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047421205.1(MYBPH):​c.112+14G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 152,130 control chromosomes in the GnomAD database, including 9,789 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.30 (9789 hom., cov: 33)
• Consequence: MYBPH XM_047421205.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.155
• Publications: 15 publications found

Genes affected

MYBPH (HGNC:7552): (myosin binding protein H) Predicted to be a structural constituent of muscle. Predicted to be involved in regulation of striated muscle contraction. Predicted to be located in myosin filament. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45556 AN: 152012 Hom.: 9756 Cov.: 33

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.278

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.300 AC: 45630 AN: 152130 Hom.: 9789 Cov.: 33 AF XY: 0.295 AC XY: 21971 AN XY: 74372

African (AFR) AF: 0.612 AC: 25369 AN: 41464

American (AMR) AF: 0.283 AC: 4326 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 708 AN: 3470

East Asian (EAS) AF: 0.222 AC: 1151 AN: 5176

South Asian (SAS) AF: 0.148 AC: 713 AN: 4820

European-Finnish (FIN) AF: 0.147 AC: 1564 AN: 10604

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11083 AN: 67994

Other (OTH) AF: 0.274 AC: 580 AN: 2114

Alfa AF: 0.235 Hom.: 821

Bravo AF: 0.326

Asia WGS AF: 0.237 AC: 822 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.84
DANN	Benign	0.66
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs883125; hg19: chr1-203146166;