rs12882548

Variant names:

• chr14-26797775-T-C
• rs12882548
• ENST00000548328.5:n.105-139T>C

Your query was ambiguous. Multiple possible variants found:

• chr14-26797775-T-C
• chr14-26797775-T-G

Variant summary

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

The ENST00000548328.5(NOVA1-DT):​n.105-139T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 152,130 control chromosomes in the GnomAD database, including 4,673 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 0.24 (4673 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: NOVA1-DT ENST00000548328.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0320
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02294	NR_110033.1	n.305+10947A>G		intron_variant	Intron 3 of 3
NOVA1-DT	NR_147061.1	n.2021-8461T>C		intron_variant	Intron 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NOVA1-DT	ENST00000548328.5	n.105-139T>C		intron_variant	Intron 2 of 3	5
LINC02294	ENST00000549330.1	n.292+10947A>G		intron_variant	Intron 3 of 3	2
NOVA1-DT	ENST00000552101.1	n.120-139T>C		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36888 AN: 152012 Hom.: 4669 Cov.: 32

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.208

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.243 AC: 36917 AN: 152130 Hom.: 4673 Cov.: 32 AF XY: 0.244 AC XY: 18129 AN XY: 74374

African (AFR) AF: 0.230 AC: 9537 AN: 41498

American (AMR) AF: 0.173 AC: 2650 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 763 AN: 3472

East Asian (EAS) AF: 0.158 AC: 816 AN: 5174

South Asian (SAS) AF: 0.322 AC: 1551 AN: 4822

European-Finnish (FIN) AF: 0.308 AC: 3264 AN: 10584

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.258 AC: 17562 AN: 67980

Other (OTH) AF: 0.215 AC: 453 AN: 2110

Alfa AF: 0.250 Hom.: 7617

Bravo AF: 0.230

Asia WGS AF: 0.263 AC: 917 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.6
DANN	Benign	0.75
PhyloP100		0.032

Splicing

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

Other links and lift over

dbSNP: rs12882548; hg19: chr14-27266981;