ENST00000556890.1:n.359-132838C>T

Variant names:

• chr14-27454979-G-A
• rs12880735
• ENST00000556890.1:n.359-132838C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000556890.1(MIR3171HG):​n.359-132838C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 152,010 control chromosomes in the GnomAD database, including 6,140 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 0.25 (6140 hom., cov: 32)
• Consequence: MIR3171HG ENST00000556890.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0290

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR3171HG	NR_148991.1	n.254-132838C>T		intron_variant	Intron 2 of 2
MIR3171HG	NR_148992.1	n.359-132838C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR3171HG	ENST00000556890.1	n.359-132838C>T		intron_variant	Intron 2 of 2	1
MIR3171HG	ENST00000553392.5	n.263-132838C>T		intron_variant	Intron 2 of 5	3
MIR3171HG	ENST00000554904.5	n.254-132838C>T		intron_variant	Intron 2 of 2	4
MIR3171HG	ENST00000555797.1	n.349-132838C>T		intron_variant	Intron 3 of 3	3

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37505 AN: 151892 Hom.: 6141 Cov.: 32

Gnomad AFR AF: 0.0591

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.0191

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.247 AC: 37497 AN: 152010 Hom.: 6140 Cov.: 32 AF XY: 0.245 AC XY: 18196 AN XY: 74286

Gnomad4 AFR AF: 0.0589

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.0187

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.359

Gnomad4 NFE AF: 0.367

Gnomad4 OTH AF: 0.248

Alfa AF: 0.327 Hom.: 4090

Bravo AF: 0.223

Asia WGS AF: 0.120 AC: 420 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12880735; hg19: chr14-27924185;