ENST00000673955.1:n.373-20569A>G

Variant names:

• chr1-180541635-A-G
• rs16856123
• ENST00000673955.1:n.373-20569A>G

Variant summary

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

The ENST00000673955.1(OVAAL):​n.373-20569A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.042 in 152,264 control chromosomes in the GnomAD database, including 373 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 0.042 (373 hom., cov: 32)
• Consequence: OVAAL ENST00000673955.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.644

Genes affected

OVAAL (HGNC:49422): (ovarian adenocarcinoma amplified long non-coding RNA)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.115 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
OVAAL	ENST00000673955.1	n.373-20569A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0419 AC: 6382 AN: 152146 Hom.: 368 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0616

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0651

Gnomad SAS AF: 0.00228

Gnomad FIN AF: 0.00669

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00104

Gnomad OTH AF: 0.0268

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0420 AC: 6402 AN: 152264 Hom.: 373 Cov.: 32 AF XY: 0.0411 AC XY: 3063 AN XY: 74466

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.0622

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.0650

Gnomad4 SAS AF: 0.00228

Gnomad4 FIN AF: 0.00669

Gnomad4 NFE AF: 0.00104

Gnomad4 OTH AF: 0.0265

Alfa AF: 0.0119 Hom.: 108

Bravo AF: 0.0525

Asia WGS AF: 0.0370 AC: 129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.7
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16856123; hg19: chr1-180510771;