ENST00000556890.1:n.358+120914C>T

Variant names:

• chr14-27535424-G-A
• rs2022896
• ENST00000556890.1:n.358+120914C>T

Variant summary

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

The ENST00000556890.1(MIR3171HG):​n.358+120914C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 152,010 control chromosomes in the GnomAD database, including 11,490 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 0.36 (11490 hom., cov: 32)
• Consequence: MIR3171HG ENST00000556890.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.428
• Publications: 3 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.58 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR3171HG	NR_148991.1		n.253+121019C>T		intron	N/A
	MIR3171HG	NR_148992.1		n.358+120914C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR3171HG	ENST00000556890.1	TSL:1	n.358+120914C>T		intron	N/A
	MIR3171HG	ENST00000553392.5	TSL:3	n.262+121019C>T		intron	N/A
	MIR3171HG	ENST00000554904.5	TSL:4	n.253+121019C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54724 AN: 151888 Hom.: 11463 Cov.: 32

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.361 AC: 54800 AN: 152010 Hom.: 11490 Cov.: 32 AF XY: 0.358 AC XY: 26610 AN XY: 74296

African (AFR) AF: 0.586 AC: 24291 AN: 41450

American (AMR) AF: 0.295 AC: 4504 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 672 AN: 3472

East Asian (EAS) AF: 0.440 AC: 2266 AN: 5150

South Asian (SAS) AF: 0.345 AC: 1664 AN: 4820

European-Finnish (FIN) AF: 0.249 AC: 2632 AN: 10580

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.260 AC: 17634 AN: 67952

Other (OTH) AF: 0.329 AC: 694 AN: 2110

Alfa AF: 0.294 Hom.: 5412

Bravo AF: 0.373

Asia WGS AF: 0.386 AC: 1340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.75
DANN	Benign	0.52
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs2022896; hg19: chr14-28004630;