ENST00000556890.1:n.358+68504T>A

Variant names:

• chr14-27587834-A-T
• rs1954673
• ENST00000556890.1:n.358+68504T>A

Variant summary

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

The ENST00000556890.1(MIR3171HG):​n.358+68504T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.68 in 151,746 control chromosomes in the GnomAD database, including 36,063 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 0.68 (36063 hom., cov: 31)
• Consequence: MIR3171HG ENST00000556890.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• Publications: 4 publications found

Genes affected

MIR3171HG (HGNC:):

LINC00645 (HGNC:44299): (long intergenic non-protein coding RNA 645)

MIR3171HG (HGNC:56193): (MIR3171 host gene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.769 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR3171HG	NR_148991.1	n.253+68609T>A		intron_variant	Intron 2 of 2
MIR3171HG	NR_148992.1	n.358+68504T>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR3171HG	ENST00000556890.1	n.358+68504T>A		intron_variant	Intron 2 of 2	1
MIR3171HG	ENST00000553392.5	n.262+68609T>A		intron_variant	Intron 2 of 5	3
MIR3171HG	ENST00000554904.5	n.253+68609T>A		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.680 AC: 103175 AN: 151626 Hom.: 36041 Cov.: 31

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.774

Gnomad ASJ AF: 0.843

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.789

Gnomad FIN AF: 0.757

Gnomad MID AF: 0.768

Gnomad NFE AF: 0.730

Gnomad OTH AF: 0.712

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

GnomAD4 genome AF: 0.680 AC: 103234 AN: 151746 Hom.: 36063 Cov.: 31 AF XY: 0.684 AC XY: 50723 AN XY: 74140

African (AFR) AF: 0.506 AC: 20960 AN: 41390

American (AMR) AF: 0.774 AC: 11799 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.843 AC: 2928 AN: 3472

East Asian (EAS) AF: 0.776 AC: 3994 AN: 5148

South Asian (SAS) AF: 0.790 AC: 3806 AN: 4818

European-Finnish (FIN) AF: 0.757 AC: 7963 AN: 10526

Middle Eastern (MID) AF: 0.754 AC: 214 AN: 284

European-Non Finnish (NFE) AF: 0.730 AC: 49566 AN: 67856

Other (OTH) AF: 0.712 AC: 1499 AN: 2104

Alfa AF: 0.631 Hom.: 1994

Bravo AF: 0.671

Asia WGS AF: 0.788 AC: 2715 AN: 3442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0020
DANN	Benign	0.54
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1954673; hg19: chr14-28057040;