rs1954673

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr14-27587834-A-C
• chr14-27587834-A-G
• chr14-27587834-A-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000556890.1(MIR3171HG):​n.358+68504T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

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+68609T>G		intron	N/A
	MIR3171HG	NR_148992.1		n.358+68504T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR3171HG	ENST00000556890.1	TSL:1	n.358+68504T>G		intron	N/A
	MIR3171HG	ENST00000553392.5	TSL:3	n.262+68609T>G		intron	N/A
	MIR3171HG	ENST00000554904.5	TSL:4	n.253+68609T>G		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0020
DANN	Benign	0.64
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;