rs4978113

Positions:

• chr9-21401107-T-C

Variant summary

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

The ENST00000698373.1(MIR31HG):​n.2439A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,164 control chromosomes in the GnomAD database, including 2,697 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 0.18 (2697 hom., cov: 32)
• Consequence: MIR31HG ENST00000698373.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

Genes affected

MIR31HG (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.21401107T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR31HG	ENST00000698373.1	n.2439A>G		non_coding_transcript_exon_variant	2/2
MIR31HG	ENST00000698342.1	n.725+1684A>G		intron_variant
MIR31HG	ENST00000698374.1	n.1118-151A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27067 AN: 152046 Hom.: 2695 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.178 AC: 27092 AN: 152164 Hom.: 2697 Cov.: 32 AF XY: 0.182 AC XY: 13567 AN XY: 74380

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.221

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.304

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.228

Gnomad4 NFE AF: 0.196

Gnomad4 OTH AF: 0.157

Alfa AF: 0.184 Hom.: 3511

Bravo AF: 0.173

Asia WGS AF: 0.247 AC: 860 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	15
DANN	Benign	0.96

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4978113; hg19: chr9-21401106;