14-27695539-C-T

Variant names:

• chr14-27695539-C-T
• rs4981658
• ENST00000555797.1:n.289-39037G>A

Variant summary

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

The ENST00000555797.1(MIR3171HG):​n.289-39037G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 152,076 control chromosomes in the GnomAD database, including 5,102 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 0.24 (5102 hom., cov: 33)
• Consequence: MIR3171HG ENST00000555797.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 5 publications found

Genes affected

MIR3171HG (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000555797.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR3171HG	ENST00000555797.1	TSL:3	n.289-39037G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36450 AN: 151958 Hom.: 5091 Cov.: 33

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.0589

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.240 AC: 36484 AN: 152076 Hom.: 5102 Cov.: 33 AF XY: 0.243 AC XY: 18051 AN XY: 74328

African (AFR) AF: 0.114 AC: 4725 AN: 41526

American (AMR) AF: 0.383 AC: 5838 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 799 AN: 3468

East Asian (EAS) AF: 0.0592 AC: 306 AN: 5168

South Asian (SAS) AF: 0.254 AC: 1223 AN: 4818

European-Finnish (FIN) AF: 0.304 AC: 3218 AN: 10572

Middle Eastern (MID) AF: 0.257 AC: 75 AN: 292

European-Non Finnish (NFE) AF: 0.287 AC: 19532 AN: 67974

Other (OTH) AF: 0.274 AC: 576 AN: 2106

Alfa AF: 0.273 Hom.: 11728

Bravo AF: 0.244

Asia WGS AF: 0.202 AC: 705 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.18
DANN	Benign	0.75
PhyloP100		-2.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4981658;

hg19: chr14-28164745;