chr14-27514296-A-G

Position:

• chr14-27514296-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_148991.1(MIR3171HG):​n.253+142147T>C variant causes a intron, non coding transcript 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 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 Benign. Variant got -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.

Transcripts

RefSeq

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

Ensembl

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

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

Gnomad4 AFR AF: 0.436

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.622

Gnomad4 SAS AF: 0.432

Gnomad4 FIN AF: 0.455

Gnomad4 NFE AF: 0.366

Gnomad4 OTH AF: 0.368

Alfa AF: 0.347 Hom.: 4541

Bravo AF: 0.393

Asia WGS AF: 0.503 AC: 1748 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.7
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;