rs884209

Positions:

• chr1-203178161-G-A
• chr1-203178161-G-C
• chr1-203178161-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047421205.1(MYBPH):​c.-998C>T variant causes a 5 prime UTR 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.46

Genes affected

MYBPH (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYBPH	XM_047421205.1	c.-998C>T		5_prime_UTR_variant	1/12		XP_047277161.1

Ensembl

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

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

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.396

Gnomad4 EAS AF: 0.323

Gnomad4 SAS AF: 0.463

Gnomad4 FIN AF: 0.552

Gnomad4 NFE AF: 0.521

Gnomad4 OTH AF: 0.408

Alfa AF: 0.452 Hom.: 4119

Bravo AF: 0.372

Asia WGS AF: 0.377 AC: 1313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs884209; hg19: chr1-203147289;