chr9-21499625-A-C

Position:

• chr9-21499625-A-C

Variant summary

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

The ENST00000304425.4(MIR31HG):​n.344-22333T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.651 in 151,930 control chromosomes in the GnomAD database, including 32,669 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 0.65 (32669 hom., cov: 31)
• Consequence: MIR31HG ENST00000304425.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.348

Genes affected

MIR31HG (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.912 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR31HG	NR_027054.2	n.311-22333T>G		intron_variant
MIR31HG	NR_152877.1	n.52-22333T>G		intron_variant
MIR31HG	NR_152878.1	n.52-22333T>G		intron_variant
MIR31HG	NR_152879.1	n.311-22333T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR31HG	ENST00000304425.4	n.344-22333T>G		intron_variant		2
MIR31HG	ENST00000654736.2	n.134-22333T>G		intron_variant
MIR31HG	ENST00000663833.2	n.123-22333T>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.651 AC: 98898 AN: 151814 Hom.: 32670 Cov.: 31

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.692

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.934

Gnomad SAS AF: 0.772

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.658

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.651 AC: 98927 AN: 151930 Hom.: 32669 Cov.: 31 AF XY: 0.655 AC XY: 48675 AN XY: 74264

Gnomad4 AFR AF: 0.573

Gnomad4 AMR AF: 0.692

Gnomad4 ASJ AF: 0.656

Gnomad4 EAS AF: 0.934

Gnomad4 SAS AF: 0.771

Gnomad4 FIN AF: 0.644

Gnomad4 NFE AF: 0.658

Gnomad4 OTH AF: 0.674

Alfa AF: 0.632 Hom.: 4115

Bravo AF: 0.654

Asia WGS AF: 0.818 AC: 2841 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7849420; hg19: chr9-21499624;