14-26937686-G-T

Variant names:

• chr14-26937686-G-T
• rs17111920
• ENST00000552303.1:n.205+94030G>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BS1 BS2

The ENST00000552303.1(MIR4307HG):​n.205+94030G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.021 in 151,804 control chromosomes in the GnomAD database, including 52 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 0.021 (52 hom., cov: 32)
• Consequence: MIR4307HG ENST00000552303.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.419
• Publications: 6 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.021 (3181/151804) while in subpopulation AFR AF = 0.0496 (2056/41456). AF 95% confidence interval is 0.0478. There are 52 homozygotes in GnomAd4. There are 1474 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 52 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000552303.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR4307HG	ENST00000552303.1	TSL:4	n.205+94030G>T		intron	N/A
	NOVA1-DT	ENST00000656336.1		n.481-196284G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0209 AC: 3173 AN: 151686 Hom.: 52 Cov.: 32

Gnomad AFR AF: 0.0496

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0139

Gnomad ASJ AF: 0.0110

Gnomad EAS AF: 0.0234

Gnomad SAS AF: 0.00145

Gnomad FIN AF: 0.00104

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00997

Gnomad OTH AF: 0.0230

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

GnomAD4 genome AF: 0.0210 AC: 3181 AN: 151804 Hom.: 52 Cov.: 32 AF XY: 0.0199 AC XY: 1474 AN XY: 74188

African (AFR) AF: 0.0496 AC: 2056 AN: 41456

American (AMR) AF: 0.0139 AC: 211 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.0110 AC: 38 AN: 3468

East Asian (EAS) AF: 0.0236 AC: 121 AN: 5122

South Asian (SAS) AF: 0.00145 AC: 7 AN: 4826

European-Finnish (FIN) AF: 0.00104 AC: 11 AN: 10596

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.00997 AC: 676 AN: 67826

Other (OTH) AF: 0.0228 AC: 48 AN: 2108

Alfa AF: 0.0141 Hom.: 46

Bravo AF: 0.0224

Asia WGS AF: 0.0120 AC: 43 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	17
DANN	Benign	0.68
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs17111920; hg19: chr14-27406892;