chr15-51180048-C-T

Position:

• chr15-51180048-C-T

Variant summary

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

The NR_146310.1(MIR4713HG):​n.195-97935C>T 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 0.581 in 152,062 control chromosomes in the GnomAD database, including 26,927 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 0.58 (26927 hom., cov: 32)
• Consequence: MIR4713HG NR_146310.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.111

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.837 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR4713HG	NR_146310.1	n.195-97935C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR4713HG	ENST00000559909.1	n.195-97935C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88223 AN: 151944 Hom.: 26886 Cov.: 32

Gnomad AFR AF: 0.743

Gnomad AMI AF: 0.628

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.858

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.581 AC: 88317 AN: 152062 Hom.: 26927 Cov.: 32 AF XY: 0.580 AC XY: 43109 AN XY: 74338

Gnomad4 AFR AF: 0.743

Gnomad4 AMR AF: 0.524

Gnomad4 ASJ AF: 0.357

Gnomad4 EAS AF: 0.858

Gnomad4 SAS AF: 0.427

Gnomad4 FIN AF: 0.571

Gnomad4 NFE AF: 0.499

Gnomad4 OTH AF: 0.528

Alfa AF: 0.509 Hom.: 9442

Bravo AF: 0.590

Asia WGS AF: 0.627 AC: 2179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.94
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1122044; hg19: chr15-51472245;