rs235858

Positions:

• chr1-171627362-G-A
• chr1-171627362-G-T

Variant summary

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

The ENST00000636697.1(MYOCOS):​c.*761G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.664 in 152,006 control chromosomes in the GnomAD database, including 33,861 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 0.66 (33857 hom., cov: 31)
  • Exomes 𝑓: 0.69 (4 hom.)
• Consequence: MYOCOS ENST00000636697.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296

Genes affected

MYOCOS (HGNC:53429): (myocilin opposite strand)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYOCOS	ENST00000636697.1	c.*761G>A		3_prime_UTR_variant	4/4	5		ENSP00000489662	P2
MYOCOS	ENST00000637303.1	c.234+770G>A		intron_variant		5		ENSP00000490048	A2

Frequencies

GnomAD3 genomes AF: 0.663 AC: 100745 AN: 151874 Hom.: 33807 Cov.: 31

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.697

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.669

GnomAD4 exome AF: 0.688 AC: 11 AN: 16 Hom.: 4 Cov.: 0 AF XY: 0.700 AC XY: 7 AN XY: 10

Gnomad4 ASJ exome AF: 0.00

Gnomad4 FIN exome AF: 0.750

Gnomad4 NFE exome AF: 0.800

GnomAD4 genome AF: 0.664 AC: 100847 AN: 151990 Hom.: 33857 Cov.: 31 AF XY: 0.664 AC XY: 49308 AN XY: 74280

Gnomad4 AFR AF: 0.775

Gnomad4 AMR AF: 0.594

Gnomad4 ASJ AF: 0.697

Gnomad4 EAS AF: 0.557

Gnomad4 SAS AF: 0.710

Gnomad4 FIN AF: 0.629

Gnomad4 NFE AF: 0.620

Gnomad4 OTH AF: 0.664

Alfa AF: 0.589 Hom.: 4784

Bravo AF: 0.658

Asia WGS AF: 0.585 AC: 2038 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.7
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs235858; hg19: chr1-171596502;