rs1956817

Variant names:

• chr14-26838608-T-C
• rs1956817
• ENST00000550024.1:n.75+1806T>C

Variant summary

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

The ENST00000550024.1(MIR4307HG):​n.75+1806T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0216 in 152,208 control chromosomes in the GnomAD database, including 59 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 0.022 (59 hom., cov: 32)
• Consequence: MIR4307HG ENST00000550024.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.809
• Publications: 0 publications found

Genes affected

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

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

ENSG00000286479 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.0501 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903296	XR_007064092.1	n.539-142A>G		intron_variant	Intron 4 of 5
LOC124903296	XR_007064093.1	n.529-142A>G		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR4307HG	ENST00000550024.1	n.75+1806T>C		intron_variant	Intron 1 of 2	3
NOVA1-DT	ENST00000656336.1	n.480+113814T>C		intron_variant	Intron 2 of 5
ENSG00000286479	ENST00000659271.2	n.412-142A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0215 AC: 3269 AN: 152090 Hom.: 60 Cov.: 32

Gnomad AFR AF: 0.0519

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0136

Gnomad ASJ AF: 0.0110

Gnomad EAS AF: 0.0210

Gnomad SAS AF: 0.00165

Gnomad FIN AF: 0.00104

Gnomad MID AF: 0.0382

Gnomad NFE AF: 0.0101

Gnomad OTH AF: 0.0235

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

GnomAD4 genome AF: 0.0216 AC: 3281 AN: 152208 Hom.: 59 Cov.: 32 AF XY: 0.0202 AC XY: 1506 AN XY: 74436

African (AFR) AF: 0.0520 AC: 2159 AN: 41542

American (AMR) AF: 0.0136 AC: 208 AN: 15288

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

East Asian (EAS) AF: 0.0213 AC: 110 AN: 5170

South Asian (SAS) AF: 0.00166 AC: 8 AN: 4830

European-Finnish (FIN) AF: 0.00104 AC: 11 AN: 10624

Middle Eastern (MID) AF: 0.0411 AC: 12 AN: 292

European-Non Finnish (NFE) AF: 0.0101 AC: 686 AN: 67974

Other (OTH) AF: 0.0232 AC: 49 AN: 2110

Alfa AF: 0.0184 Hom.: 5

Bravo AF: 0.0236

Asia WGS AF: 0.0130 AC: 45 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.61
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs1956817; hg19: chr14-27307814;