14-27514296-A-G

Variant names:

• chr14-27514296-A-G
• rs12587505
• ENST00000556890.1:n.358+142042T>C

Variant summary

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

The ENST00000556890.1(MIR3171HG):​n.358+142042T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 152,072 control chromosomes in the GnomAD database, including 12,399 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 0.40 (12399 hom., cov: 32)
• Consequence: MIR3171HG ENST00000556890.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.285
• Publications: 2 publications found

Genes affected

MIR3171HG (HGNC:):

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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.604 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000556890.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR3171HG	NR_148991.1		n.253+142147T>C		intron	N/A
	MIR3171HG	NR_148992.1		n.358+142042T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR3171HG	ENST00000556890.1	TSL:1	n.358+142042T>C		intron	N/A
	MIR3171HG	ENST00000553392.5	TSL:3	n.262+142147T>C		intron	N/A
	MIR3171HG	ENST00000554904.5	TSL:4	n.253+142147T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60607 AN: 151952 Hom.: 12379 Cov.: 32

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.622

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.399 AC: 60666 AN: 152072 Hom.: 12399 Cov.: 32 AF XY: 0.403 AC XY: 29939 AN XY: 74326

African (AFR) AF: 0.436 AC: 18102 AN: 41482

American (AMR) AF: 0.351 AC: 5369 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 954 AN: 3468

East Asian (EAS) AF: 0.622 AC: 3208 AN: 5156

South Asian (SAS) AF: 0.432 AC: 2078 AN: 4810

European-Finnish (FIN) AF: 0.455 AC: 4811 AN: 10570

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.366 AC: 24861 AN: 67986

Other (OTH) AF: 0.368 AC: 776 AN: 2110

Alfa AF: 0.351 Hom.: 5154

Bravo AF: 0.393

Asia WGS AF: 0.503 AC: 1748 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.7
DANN	Benign	0.63
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs12587505; hg19: chr14-27983502;