rs10483331

Variant names:

• chr14-27007762-T-C
• rs10483331
• ENST00000552303.1:n.206-69476T>C

Variant summary

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

The ENST00000552303.1(MIR4307HG):​n.206-69476T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 152,002 control chromosomes in the GnomAD database, including 16,354 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 0.45 (16354 hom., cov: 32)
• Consequence: MIR4307HG ENST00000552303.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.519
• Publications: 1 publications found

Genes affected

MIR4307HG (HGNC:52004): (MIR4307 host gene)

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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.528 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR4307HG	ENST00000552303.1	n.206-69476T>C		intron_variant	Intron 1 of 5	4
NOVA1-DT	ENST00000656336.1	n.481-126208T>C		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.448 AC: 68046 AN: 151884 Hom.: 16347 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.448 AC: 68072 AN: 152002 Hom.: 16354 Cov.: 32 AF XY: 0.448 AC XY: 33253 AN XY: 74302

African (AFR) AF: 0.276 AC: 11446 AN: 41484

American (AMR) AF: 0.523 AC: 7987 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.590 AC: 2045 AN: 3468

East Asian (EAS) AF: 0.231 AC: 1189 AN: 5138

South Asian (SAS) AF: 0.471 AC: 2272 AN: 4820

European-Finnish (FIN) AF: 0.481 AC: 5081 AN: 10554

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.533 AC: 36218 AN: 67962

Other (OTH) AF: 0.476 AC: 1001 AN: 2104

Alfa AF: 0.455 Hom.: 2621

Bravo AF: 0.443

Asia WGS AF: 0.373 AC: 1299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.9
DANN	Benign	0.43
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs10483331; hg19: chr14-27476968;