rs7849420

Variant names:

• chr9-21499625-A-C
• rs7849420
• ENST00000304425.4:n.344-22333T>G

Your query was ambiguous. Multiple possible variants found:

• chr9-21499625-A-C
• chr9-21499625-A-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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=-0.94).
• 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 rank	MANE	Protein	UniProt
MIR31HG	NR_027054.2	n.311-22333T>G		intron_variant	Intron 1 of 3
MIR31HG	NR_152877.1	n.52-22333T>G		intron_variant	Intron 1 of 3
MIR31HG	NR_152878.1	n.52-22333T>G		intron_variant	Intron 1 of 2
MIR31HG	NR_152879.1	n.311-22333T>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR31HG	ENST00000304425.4	n.344-22333T>G		intron_variant	Intron 1 of 3	2
MIR31HG	ENST00000654736.2	n.134-22333T>G		intron_variant	Intron 1 of 3
MIR31HG	ENST00000663833.2	n.123-22333T>G		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.573 AC: 23721 AN: 41374

American (AMR) AF: 0.692 AC: 10570 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.656 AC: 2278 AN: 3472

East Asian (EAS) AF: 0.934 AC: 4839 AN: 5180

South Asian (SAS) AF: 0.771 AC: 3711 AN: 4816

European-Finnish (FIN) AF: 0.644 AC: 6789 AN: 10550

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.658 AC: 44732 AN: 67952

Other (OTH) AF: 0.674 AC: 1419 AN: 2106

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
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs7849420; hg19: chr9-21499624;