chr14-26965634-T-C

Variant names:

• chr14-26965634-T-C
• rs4328361
• ENST00000552303.1:n.206-111604T>C

Variant summary

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

The ENST00000552303.1(MIR4307HG):​n.206-111604T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.883 in 152,182 control chromosomes in the GnomAD database, including 60,081 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 0.88 (60081 hom., cov: 32)
• Consequence: MIR4307HG ENST00000552303.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 0 publications found

Genes affected

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

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

LOC105370419 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370419	XR_001750687.1	n.427-1574T>C		intron_variant	Intron 1 of 2
LOC105370419	XR_001750688.1	n.1940-1574T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR4307HG	ENST00000552303.1	n.206-111604T>C		intron_variant	Intron 1 of 5	4
NOVA1-DT	ENST00000656336.1	n.481-168336T>C		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.884 AC: 134353 AN: 152064 Hom.: 60042 Cov.: 32

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.963

Gnomad AMR AF: 0.936

Gnomad ASJ AF: 0.943

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.892

Gnomad FIN AF: 0.959

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.938

Gnomad OTH AF: 0.902

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

GnomAD4 genome AF: 0.883 AC: 134446 AN: 152182 Hom.: 60081 Cov.: 32 AF XY: 0.885 AC XY: 65884 AN XY: 74426

African (AFR) AF: 0.732 AC: 30353 AN: 41464

American (AMR) AF: 0.937 AC: 14327 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.943 AC: 3274 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5155 AN: 5158

South Asian (SAS) AF: 0.891 AC: 4307 AN: 4832

European-Finnish (FIN) AF: 0.959 AC: 10177 AN: 10616

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.938 AC: 63793 AN: 68026

Other (OTH) AF: 0.904 AC: 1912 AN: 2116

Alfa AF: 0.900 Hom.: 8033

Bravo AF: 0.877

Asia WGS AF: 0.951 AC: 3308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.60
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs4328361; hg19: chr14-27434840;