14-26654208-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

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

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000547786.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NOVA1-DT	NR_147061.1		n.1680+16875C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NOVA1-DT	ENST00000547786.1	TSL:3	n.277-9405C>T		intron	N/A
	NOVA1-DT	ENST00000552826.5	TSL:5	n.93+16875C>T		intron	N/A
	NOVA1-DT	ENST00000653681.1		n.320-9405C>T		intron	N/A

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

African (AFR) AF: 0.538 AC: 22239 AN: 41368

American (AMR) AF: 0.700 AC: 10630 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 1995 AN: 3462

East Asian (EAS) AF: 0.496 AC: 2560 AN: 5160

South Asian (SAS) AF: 0.604 AC: 2901 AN: 4804

European-Finnish (FIN) AF: 0.688 AC: 7257 AN: 10548

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.674 AC: 45621 AN: 67648

Other (OTH) AF: 0.648 AC: 1357 AN: 2094

Alfa AF: 0.636 Hom.: 10376

Bravo AF: 0.630

Asia WGS AF: 0.529 AC: 1828 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.2
DANN	Benign	0.65
PhyloP100		-0.23

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1955850;

hg19: chr14-27123414;