19-4768905-A-G

Variant names:

• chr19-4768905-A-G
• rs879564
• ENST00000317292.10:n.-222A>G

Variant summary

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

The ENST00000317292.10(MIR7-3HG):​n.-222A>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 152,078 control chromosomes in the GnomAD database, including 13,519 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 0.41 (13519 hom., cov: 32)
• Consequence: MIR7-3HG ENST00000317292.10 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66
• Publications: 17 publications found

Genes affected

MIR7-3HG (HGNC:30049): (MIR7-3 host gene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR7-3HG	NR_027148.1	n.-200A>G		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR7-3HG	ENST00000317292.10	n.-222A>G		upstream_gene_variant		1
MIR7-3HG	ENST00000592709.7	n.-227A>G		upstream_gene_variant		1
MIR7-3HG	ENST00000586721.8	n.-227A>G		upstream_gene_variant		2

Frequencies

GnomAD3 genomes AF: 0.408 AC: 62067 AN: 151960 Hom.: 13482 Cov.: 32

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.409 AC: 62160 AN: 152078 Hom.: 13519 Cov.: 32 AF XY: 0.406 AC XY: 30190 AN XY: 74368

African (AFR) AF: 0.545 AC: 22575 AN: 41456

American (AMR) AF: 0.363 AC: 5546 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.338 AC: 1171 AN: 3468

East Asian (EAS) AF: 0.100 AC: 519 AN: 5180

South Asian (SAS) AF: 0.325 AC: 1569 AN: 4822

European-Finnish (FIN) AF: 0.356 AC: 3763 AN: 10582

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.379 AC: 25748 AN: 67970

Other (OTH) AF: 0.420 AC: 888 AN: 2114

Alfa AF: 0.389 Hom.: 35794

Bravo AF: 0.411

Asia WGS AF: 0.255 AC: 887 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.047
DANN	Benign	0.52
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs879564; hg19: chr19-4768917;