ENST00000656336.1:n.550-19264C>A

Variant names:

• chr14-27186573-C-A
• rs17112354
• ENST00000656336.1:n.550-19264C>A

Variant summary

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

The ENST00000656336.1(NOVA1-DT):​n.550-19264C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0696 in 151,788 control chromosomes in the GnomAD database, including 520 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 0.070 (520 hom., cov: 32)
• Consequence: NOVA1-DT ENST00000656336.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0810
• Publications: 2 publications found

Genes affected

NOVA1-DT (HGNC:19827): (NOVA1 divergent transcript)

LOC105370420 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370420	XR_001750686.2	n.133-19264C>A		intron_variant	Intron 2 of 3
LOC105370420	XR_943662.3	n.265-19264C>A		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NOVA1-DT	ENST00000656336.1	n.550-19264C>A		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.0696 AC: 10562 AN: 151670 Hom.: 521 Cov.: 32

Gnomad AFR AF: 0.0181

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.0673

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.0686

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0769

Gnomad OTH AF: 0.0796

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

GnomAD4 genome AF: 0.0696 AC: 10559 AN: 151788 Hom.: 520 Cov.: 32 AF XY: 0.0732 AC XY: 5429 AN XY: 74186

African (AFR) AF: 0.0181 AC: 752 AN: 41532

American (AMR) AF: 0.117 AC: 1773 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.0673 AC: 233 AN: 3464

East Asian (EAS) AF: 0.116 AC: 601 AN: 5160

South Asian (SAS) AF: 0.217 AC: 1046 AN: 4830

European-Finnish (FIN) AF: 0.0686 AC: 725 AN: 10570

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0769 AC: 5206 AN: 67708

Other (OTH) AF: 0.0806 AC: 170 AN: 2108

Alfa AF: 0.0747 Hom.: 839

Bravo AF: 0.0654

Asia WGS AF: 0.174 AC: 602 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.8
DANN	Benign	0.62
PhyloP100		0.081

Splicing

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

Other links and lift over

dbSNP: rs17112354; hg19: chr14-27655779;