rs16856123

Variant names:

• chr1-180541635-A-G
• rs16856123
• ENST00000818479.1:n.960T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000818479.1(ENSG00000306434):​n.960T>C variant causes a non coding transcript exon 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: ENSG00000306434 ENST00000818479.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.644
• Publications: 1 publications found

Genes affected

ENSG00000306434 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000306434	ENST00000818479.1	n.960T>C		non_coding_transcript_exon_variant	Exon 3 of 3
OVAAL	ENST00000673955.1	n.373-20569A>G		intron_variant	Intron 1 of 2
ENSG00000306434	ENST00000818476.1	n.126-19868T>C		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.118 AC: 4904 AN: 41526

American (AMR) AF: 0.0622 AC: 951 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.0650 AC: 337 AN: 5182

South Asian (SAS) AF: 0.00228 AC: 11 AN: 4828

European-Finnish (FIN) AF: 0.00669 AC: 71 AN: 10616

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.00104 AC: 71 AN: 68032

Other (OTH) AF: 0.0265 AC: 56 AN: 2114

Alfa AF: 0.0168 Hom.: 200

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
PhyloP100		0.64

Splicing

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

Other links and lift over

dbSNP: rs16856123; hg19: chr1-180510771;