rs12587505

chr14-27514296-A-Cchr14-27514296-A-Gchr14-27514296-A-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NR_148991.1(MIR3171HG):n.253+142147T>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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: 32)
• Consequence: MIR3171HG NR_148991.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.285

Genes affected

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

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR3171HG	NR_148991.1	n.253+142147T>G		intron_variant, non_coding_transcript_variant
MIR3171HG	NR_148992.1	n.358+142042T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR3171HG	ENST00000555797.1	n.348+142147T>G		intron_variant, non_coding_transcript_variant		3
MIR3171HG	ENST00000556890.1	n.358+142042T>G		intron_variant, non_coding_transcript_variant		1
MIR3171HG	ENST00000553392.5	n.262+142147T>G		intron_variant, non_coding_transcript_variant		3
MIR3171HG	ENST00000554904.5	n.253+142147T>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	2.5
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12587505; hg19: chr14-27983502;