rs883125

chr1-203177038-C-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

MYBPH (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYBPH	XM_047421205.1	c.112+14G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.612

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.222

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.274

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.84
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs883125; hg19: chr1-203146166;