chr14-26790837-T-A

Variant names:

• chr14-26790837-T-A
• rs1951082
• ENST00000548328.5:n.105-7077T>A

Variant summary

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

The ENST00000548328.5(NOVA1-DT):​n.105-7077T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 151,732 control chromosomes in the GnomAD database, including 21,119 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 0.49 (21119 hom., cov: 29)
• Consequence: NOVA1-DT ENST00000548328.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.376
• Publications: 13 publications found

Genes affected

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

LINC02294 (HGNC:53210): (long intergenic non-protein coding RNA 2294)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02294	NR_110033.1	n.306-15138A>T		intron_variant	Intron 3 of 3
NOVA1-DT	NR_147061.1	n.2020+8629T>A		intron_variant	Intron 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NOVA1-DT	ENST00000548328.5	n.105-7077T>A		intron_variant	Intron 2 of 3	5
LINC02294	ENST00000549330.1	n.293-15138A>T		intron_variant	Intron 3 of 3	2
NOVA1-DT	ENST00000552101.1	n.42-6654T>A		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74648 AN: 151614 Hom.: 21117 Cov.: 29

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.819

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.492 AC: 74647 AN: 151732 Hom.: 21119 Cov.: 29 AF XY: 0.499 AC XY: 36938 AN XY: 74092

African (AFR) AF: 0.203 AC: 8422 AN: 41414

American (AMR) AF: 0.639 AC: 9716 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.476 AC: 1649 AN: 3466

East Asian (EAS) AF: 0.818 AC: 4197 AN: 5128

South Asian (SAS) AF: 0.524 AC: 2512 AN: 4794

European-Finnish (FIN) AF: 0.609 AC: 6402 AN: 10514

Middle Eastern (MID) AF: 0.441 AC: 128 AN: 290

European-Non Finnish (NFE) AF: 0.589 AC: 39988 AN: 67902

Other (OTH) AF: 0.528 AC: 1110 AN: 2104

Alfa AF: 0.556 Hom.: 12322

Bravo AF: 0.483

Asia WGS AF: 0.609 AC: 2116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.1
DANN	Benign	0.80
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs1951082; hg19: chr14-27260043;