XM_047421205.1:c.-998C>T

Variant names:

• chr1-203178161-G-A
• rs884209
• XM_047421205.1:c.-998C>T

Variant summary

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

The XM_047421205.1(MYBPH):​c.-998C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.402 in 152,114 control chromosomes in the GnomAD database, including 13,918 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 0.40 (13918 hom., cov: 32)
• Consequence: MYBPH XM_047421205.1 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.46
• Publications: 8 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.517 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: 0.402 AC: 61110 AN: 151996 Hom.: 13917 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.608

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.402 AC: 61124 AN: 152114 Hom.: 13918 Cov.: 32 AF XY: 0.403 AC XY: 29939 AN XY: 74352

African (AFR) AF: 0.190 AC: 7867 AN: 41500

American (AMR) AF: 0.338 AC: 5173 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1375 AN: 3472

East Asian (EAS) AF: 0.323 AC: 1673 AN: 5176

South Asian (SAS) AF: 0.463 AC: 2235 AN: 4826

European-Finnish (FIN) AF: 0.552 AC: 5832 AN: 10556

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.521 AC: 35426 AN: 67980

Other (OTH) AF: 0.408 AC: 860 AN: 2110

Alfa AF: 0.439 Hom.: 4395

Bravo AF: 0.372

Asia WGS AF: 0.377 AC: 1313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.2
DANN	Benign	0.70
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs884209; hg19: chr1-203147289;