14-26654208-C-T

Variant names:

• chr14-26654208-C-T
• rs1955850
• ENST00000547786.1:n.277-9405C>T

Variant summary

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

The ENST00000547786.1(NOVA1-DT):​n.277-9405C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.629 in 151,480 control chromosomes in the GnomAD database, including 30,360 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 0.63 (30360 hom., cov: 31)
• Consequence: NOVA1-DT ENST00000547786.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.225

Genes affected

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

ENSG00000258081 (HGNC:):

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 (AMR) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NOVA1-DT	NR_147061.1	n.1680+16875C>T		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NOVA1-DT	ENST00000547786.1	n.277-9405C>T		intron_variant	Intron 2 of 3	3
NOVA1-DT	ENST00000552826.5	n.93+16875C>T		intron_variant	Intron 1 of 3	5
NOVA1-DT	ENST00000653681.1	n.320-9405C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.629 AC: 95261 AN: 151362 Hom.: 30345 Cov.: 31

Gnomad AFR AF: 0.538

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.700

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.649

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

GnomAD4 genome AF: 0.629 AC: 95319 AN: 151480 Hom.: 30360 Cov.: 31 AF XY: 0.631 AC XY: 46717 AN XY: 74002

Gnomad4 AFR AF: 0.538

Gnomad4 AMR AF: 0.700

Gnomad4 ASJ AF: 0.576

Gnomad4 EAS AF: 0.496

Gnomad4 SAS AF: 0.604

Gnomad4 FIN AF: 0.688

Gnomad4 NFE AF: 0.674

Gnomad4 OTH AF: 0.648

Alfa AF: 0.635 Hom.: 9069

Bravo AF: 0.630

Asia WGS AF: 0.529 AC: 1828 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.2
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1955850; hg19: chr14-27123414;