chr9-21425084-G-A

Variant names:

• chr9-21425084-G-A
• rs7871767
• ENST00000698343.1:n.103-4392C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000698343.1(MIR31HG):​n.103-4392C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 152,014 control chromosomes in the GnomAD database, including 7,967 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 0.28 (7967 hom., cov: 32)
• Consequence: MIR31HG ENST00000698343.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.858
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR31HG	ENST00000698343.1	n.103-4392C>T		intron_variant	Intron 1 of 4
MIR31HG	ENST00000698344.1	n.497-4392C>T		intron_variant	Intron 2 of 3
MIR31HG	ENST00000698345.1	n.255-4392C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.283 AC: 42926 AN: 151894 Hom.: 7932 Cov.: 32

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.283 AC: 43017 AN: 152014 Hom.: 7967 Cov.: 32 AF XY: 0.281 AC XY: 20868 AN XY: 74312

African (AFR) AF: 0.528 AC: 21906 AN: 41460

American (AMR) AF: 0.240 AC: 3668 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 582 AN: 3472

East Asian (EAS) AF: 0.263 AC: 1363 AN: 5180

South Asian (SAS) AF: 0.310 AC: 1495 AN: 4818

European-Finnish (FIN) AF: 0.165 AC: 1742 AN: 10568

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11568 AN: 67938

Other (OTH) AF: 0.233 AC: 492 AN: 2114

Alfa AF: 0.231 Hom.: 652

Bravo AF: 0.296

Asia WGS AF: 0.283 AC: 984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.0
DANN	Benign	0.59
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs7871767; hg19: chr9-21425083;