9-21470998-C-T

Variant summary

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

The NR_152878.1(MIR31HG):n.175+6171G>A 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 0.246 in 151,968 control chromosomes in the GnomAD database, including 6,920 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 0.25 (6920 hom., cov: 32)
• Consequence: MIR31HG NR_152878.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.991

Genes affected

MIR31HG (HGNC:37187): (MIR31 host gene) This gene produces a long non-coding RNA that acts as a host gene for miR-31. This transcript may be involved in cellular pluripotency and regulate the differentiation of myoblasts and other tissues. This RNA was found to interact with Polycomb repressive proteins to repression transcription of genes involves in cell senescence. [provided by RefSeq, Dec 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR31HG	NR_152878.1	n.175+6171G>A		intron_variant, non_coding_transcript_variant
MIR31HG	NR_027054.2	n.571+5901G>A		intron_variant, non_coding_transcript_variant
MIR31HG	NR_152877.1	n.312+5901G>A		intron_variant, non_coding_transcript_variant
MIR31HG	NR_152879.1	n.434+6171G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR31HG	ENST00000698343.1	n.103-50306G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37237 AN: 151850 Hom.: 6890 Cov.: 32

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.246 AC: 37322 AN: 151968 Hom.: 6920 Cov.: 32 AF XY: 0.248 AC XY: 18381 AN XY: 74264

Gnomad4 AFR AF: 0.509

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.200

Alfa AF: 0.130 Hom.: 2718

Bravo AF: 0.259

Asia WGS AF: 0.279 AC: 969 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.31
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: rs7861480; hg19: chr9-21470997;