rs16964189

Positions:

• chr15-51202040-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.195-75943C>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 0.201 in 152,106 control chromosomes in the GnomAD database, including 3,091 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 0.20 (3091 hom., cov: 32)
• Consequence: MIR4713HG NR_146310.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240

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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR4713HG	NR_146310.1	n.195-75943C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR4713HG	ENST00000559909.1	n.195-75943C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30502 AN: 151990 Hom.: 3089 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.201 AC: 30512 AN: 152106 Hom.: 3091 Cov.: 32 AF XY: 0.202 AC XY: 15050 AN XY: 74368

Gnomad4 AFR AF: 0.187

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.240

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.289

Gnomad4 FIN AF: 0.196

Gnomad4 NFE AF: 0.211

Gnomad4 OTH AF: 0.199

Alfa AF: 0.211 Hom.: 3452

Bravo AF: 0.194

Asia WGS AF: 0.237 AC: 824 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.5
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16964189; hg19: chr15-51494237;