19-4768905-A-G

Variant names:

• chr19-4768905-A-G
• rs879564
• ENST00000317292.9:n.-227A>G

Variant summary

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

The ENST00000317292.9(MIR7-3HG):​n.-227A>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 ENST00000317292.9 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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	ENST00000317292.9	n.-227A>G		upstream_gene_variant		1
MIR7-3HG	ENST00000592709.6	n.-228A>G		upstream_gene_variant		1
MIR7-3HG	ENST00000586721.7	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

Gnomad4 AFR AF: 0.545

Gnomad4 AMR AF: 0.363

Gnomad4 ASJ AF: 0.338

Gnomad4 EAS AF: 0.100

Gnomad4 SAS AF: 0.325

Gnomad4 FIN AF: 0.356

Gnomad4 NFE AF: 0.379

Gnomad4 OTH AF: 0.420

Alfa AF: 0.380 Hom.: 21389

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs879564; hg19: chr19-4768917;