chr1-171627362-G-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.750 AC: 3 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.800 AC: 8 AN: 10

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.775 AC: 32117 AN: 41458

American (AMR) AF: 0.594 AC: 9074 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.697 AC: 2417 AN: 3470

East Asian (EAS) AF: 0.557 AC: 2876 AN: 5162

South Asian (SAS) AF: 0.710 AC: 3421 AN: 4818

European-Finnish (FIN) AF: 0.629 AC: 6630 AN: 10544

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.620 AC: 42127 AN: 67962

Other (OTH) AF: 0.664 AC: 1398 AN: 2106

Alfa AF: 0.612 Hom.: 9137

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
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs235858; hg19: chr1-171596502;