rs7048384

Positions:

• chr9-21461791-C-T

Variant summary

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

The ENST00000304425.4(MIR31HG):​n.605-5847G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0558 in 152,002 control chromosomes in the GnomAD database, including 511 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 0.056 (511 hom., cov: 32)
• Consequence: MIR31HG ENST00000304425.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.203

Genes affected

MIR31HG (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR31HG	NR_027054.2	n.572-5847G>A		intron_variant
MIR31HG	NR_152877.1	n.313-5847G>A		intron_variant
MIR31HG	NR_152878.1	n.176-5847G>A		intron_variant
MIR31HG	NR_152879.1	n.435-5847G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR31HG	ENST00000304425.4	n.605-5847G>A		intron_variant		2
MIR31HG	ENST00000654736.2	n.395-5847G>A		intron_variant
MIR31HG	ENST00000663833.2	n.247-5847G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0558 AC: 8476 AN: 151884 Hom.: 509 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0736

Gnomad ASJ AF: 0.0150

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.0184

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.00611

Gnomad OTH AF: 0.0500

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

GnomAD4 genome AF: 0.0558 AC: 8485 AN: 152002 Hom.: 511 Cov.: 32 AF XY: 0.0594 AC XY: 4417 AN XY: 74324

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.0738

Gnomad4 ASJ AF: 0.0150

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.0184

Gnomad4 NFE AF: 0.00611

Gnomad4 OTH AF: 0.0490

Alfa AF: 0.0321 Hom.: 32

Bravo AF: 0.0607

Asia WGS AF: 0.134 AC: 465 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7048384; hg19: chr9-21461790;