rs10491569

Positions:

• chr9-21456777-G-A

Variant summary

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

The ENST00000304425.4(MIR31HG):​n.605-833C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 152,104 control chromosomes in the GnomAD database, including 4,499 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 0.24 (4499 hom., cov: 32)
• Consequence: MIR31HG ENST00000304425.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97

Genes affected

MIR31HG (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR31HG	NR_027054.2	n.572-833C>T		intron_variant
MIR31HG	NR_152877.1	n.313-833C>T		intron_variant
MIR31HG	NR_152878.1	n.176-833C>T		intron_variant
MIR31HG	NR_152879.1	n.435-833C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR31HG	ENST00000304425.4	n.605-833C>T		intron_variant		2
MIR31HG	ENST00000654736.2	n.395-833C>T		intron_variant
MIR31HG	ENST00000663833.2	n.247-833C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36453 AN: 151984 Hom.: 4497 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.240 AC: 36470 AN: 152104 Hom.: 4499 Cov.: 32 AF XY: 0.239 AC XY: 17791 AN XY: 74344

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.269

Gnomad4 EAS AF: 0.173

Gnomad4 SAS AF: 0.207

Gnomad4 FIN AF: 0.288

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.276

Alfa AF: 0.266 Hom.: 5451

Bravo AF: 0.234

Asia WGS AF: 0.206 AC: 718 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.14
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10491569; hg19: chr9-21456776; COSMIC: COSV58643580;