rs6475535

Variant names:

• chr9-21450475-G-C
• rs6475535
• ENST00000698343.1:n.103-29783C>G

Variant summary

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

The ENST00000698343.1(MIR31HG):​n.103-29783C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 152,130 control chromosomes in the GnomAD database, including 5,607 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 (5607 hom., cov: 32)
• Consequence: MIR31HG ENST00000698343.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.717
• 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.417 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.103-29783C>G		intron_variant	Intron 1 of 4
MIR31HG	ENST00000698344.1	n.496+26694C>G		intron_variant	Intron 2 of 3
MIR31HG	ENST00000698345.1	n.254+26694C>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36507 AN: 152010 Hom.: 5576 Cov.: 32

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.241 AC: 36588 AN: 152130 Hom.: 5607 Cov.: 32 AF XY: 0.242 AC XY: 17970 AN XY: 74374

African (AFR) AF: 0.422 AC: 17507 AN: 41456

American (AMR) AF: 0.231 AC: 3539 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 512 AN: 3468

East Asian (EAS) AF: 0.262 AC: 1353 AN: 5170

South Asian (SAS) AF: 0.310 AC: 1499 AN: 4828

European-Finnish (FIN) AF: 0.177 AC: 1876 AN: 10592

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9682 AN: 68006

Other (OTH) AF: 0.198 AC: 417 AN: 2108

Alfa AF: 0.0974 Hom.: 139

Bravo AF: 0.246

Asia WGS AF: 0.279 AC: 968 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	0.86
DANN	Benign	0.53
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs6475535; hg19: chr9-21450474;