rs235858

Variant names:

• chr1-171627362-G-A
• rs235858
• ENST00000636697.1:c.*761G>A

Your query was ambiguous. Multiple possible variants found:

• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYOCOS	ENST00000636697.1	c.*761G>A		3_prime_UTR_variant	Exon 4 of 4	5		ENSP00000489662.1
MYOCOS	ENST00000637303.1	c.234+770G>A		intron_variant	Intron 3 of 3	5		ENSP00000490048.1

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;