chr9-21467713-A-G

Variant names:

• chr9-21467713-A-G
• rs1888888
• ENST00000304425.4:n.604+9186T>C

Variant summary

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

The ENST00000304425.4(MIR31HG):​n.604+9186T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.962 in 152,326 control chromosomes in the GnomAD database, including 70,570 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 0.96 (70570 hom., cov: 32)
• Consequence: MIR31HG ENST00000304425.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350

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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.981 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR31HG	NR_027054.2	n.571+9186T>C		intron_variant	Intron 3 of 3
MIR31HG	NR_152877.1	n.312+9186T>C		intron_variant	Intron 3 of 3
MIR31HG	NR_152878.1	n.175+9456T>C		intron_variant	Intron 2 of 2
MIR31HG	NR_152879.1	n.434+9456T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR31HG	ENST00000304425.4	n.604+9186T>C		intron_variant	Intron 3 of 3	2
MIR31HG	ENST00000654736.2	n.394+9186T>C		intron_variant	Intron 3 of 3
MIR31HG	ENST00000663833.2	n.246+9456T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.962 AC: 146459 AN: 152208 Hom.: 70510 Cov.: 32

Gnomad AFR AF: 0.989

Gnomad AMI AF: 0.990

Gnomad AMR AF: 0.976

Gnomad ASJ AF: 0.985

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.995

Gnomad FIN AF: 0.955

Gnomad MID AF: 0.994

Gnomad NFE AF: 0.936

Gnomad OTH AF: 0.977

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

GnomAD4 genome AF: 0.962 AC: 146578 AN: 152326 Hom.: 70570 Cov.: 32 AF XY: 0.965 AC XY: 71873 AN XY: 74502

Gnomad4 AFR AF: 0.989

Gnomad4 AMR AF: 0.976

Gnomad4 ASJ AF: 0.985

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.995

Gnomad4 FIN AF: 0.955

Gnomad4 NFE AF: 0.936

Gnomad4 OTH AF: 0.977

Alfa AF: 0.944 Hom.: 8426

Bravo AF: 0.966

Asia WGS AF: 0.995 AC: 3459 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.8
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1888888; hg19: chr9-21467712;