chr15-51203633-A-G

Position:

• chr15-51203633-A-G

Variant summary

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

The NR_146310.1(MIR4713HG):​n.195-74350A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.789 in 152,078 control chromosomes in the GnomAD database, including 47,473 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 0.79 (47473 hom., cov: 31)
• Consequence: MIR4713HG NR_146310.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

Genes affected

MIR4713HG (HGNC:53124): (MIR4713 host gene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR4713HG	NR_146310.1	n.195-74350A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR4713HG	ENST00000559909.1	n.195-74350A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.789 AC: 119864 AN: 151960 Hom.: 47449 Cov.: 31

Gnomad AFR AF: 0.755

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.749

Gnomad ASJ AF: 0.860

Gnomad EAS AF: 0.693

Gnomad SAS AF: 0.796

Gnomad FIN AF: 0.804

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.820

Gnomad OTH AF: 0.776

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

GnomAD4 genome AF: 0.789 AC: 119936 AN: 152078 Hom.: 47473 Cov.: 31 AF XY: 0.789 AC XY: 58636 AN XY: 74338

Gnomad4 AFR AF: 0.755

Gnomad4 AMR AF: 0.748

Gnomad4 ASJ AF: 0.860

Gnomad4 EAS AF: 0.693

Gnomad4 SAS AF: 0.797

Gnomad4 FIN AF: 0.804

Gnomad4 NFE AF: 0.820

Gnomad4 OTH AF: 0.775

Alfa AF: 0.816 Hom.: 32978

Bravo AF: 0.781

Asia WGS AF: 0.715 AC: 2488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.77
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs934632; hg19: chr15-51495830;