rs4775919

Positions:

• chr15-51153712-G-A
• chr15-51153712-G-C
• chr15-51153712-G-T

Variant summary

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

The NR_146310.1(MIR4713HG):​n.194+116031G>A 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 0.833 in 152,044 control chromosomes in the GnomAD database, including 53,013 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 0.83 (53013 hom., cov: 30)
• Consequence: MIR4713HG NR_146310.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.96 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR4713HG	NR_146310.1	n.194+116031G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR4713HG	ENST00000559909.1	n.194+116031G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.833 AC: 126568 AN: 151926 Hom.: 52956 Cov.: 30

Gnomad AFR AF: 0.814

Gnomad AMI AF: 0.865

Gnomad AMR AF: 0.747

Gnomad ASJ AF: 0.816

Gnomad EAS AF: 0.983

Gnomad SAS AF: 0.815

Gnomad FIN AF: 0.885

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.846

Gnomad OTH AF: 0.817

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

GnomAD4 genome AF: 0.833 AC: 126688 AN: 152044 Hom.: 53013 Cov.: 30 AF XY: 0.833 AC XY: 61939 AN XY: 74320

Gnomad4 AFR AF: 0.815

Gnomad4 AMR AF: 0.747

Gnomad4 ASJ AF: 0.816

Gnomad4 EAS AF: 0.983

Gnomad4 SAS AF: 0.816

Gnomad4 FIN AF: 0.885

Gnomad4 NFE AF: 0.846

Gnomad4 OTH AF: 0.819

Alfa AF: 0.838 Hom.: 24002

Bravo AF: 0.821

Asia WGS AF: 0.902 AC: 3139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.0
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4775919; hg19: chr15-51445909;