15-51199657-T-C

Variant names:

• chr15-51199657-T-C
• rs9972359
• ENST00000559909.1:n.195-78326T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000559909.1(MIR4713HG):​n.195-78326T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.522 in 152,004 control chromosomes in the GnomAD database, including 22,554 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 0.52 (22554 hom., cov: 32)
• Consequence: MIR4713HG ENST00000559909.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.360
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR4713HG	NR_146310.1	n.195-78326T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR4713HG	ENST00000559909.1	n.195-78326T>C		intron_variant	Intron 1 of 2	4
MIR4713HG	ENST00000805692.1	n.279-78326T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.522 AC: 79307 AN: 151886 Hom.: 22515 Cov.: 32

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.539

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.569

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.522 AC: 79397 AN: 152004 Hom.: 22554 Cov.: 32 AF XY: 0.520 AC XY: 38625 AN XY: 74266

African (AFR) AF: 0.751 AC: 31172 AN: 41496

American (AMR) AF: 0.405 AC: 6193 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.338 AC: 1172 AN: 3470

East Asian (EAS) AF: 0.569 AC: 2934 AN: 5152

South Asian (SAS) AF: 0.266 AC: 1276 AN: 4796

European-Finnish (FIN) AF: 0.541 AC: 5709 AN: 10554

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.433 AC: 29397 AN: 67944

Other (OTH) AF: 0.453 AC: 956 AN: 2110

Alfa AF: 0.444 Hom.: 29540

Bravo AF: 0.527

Asia WGS AF: 0.431 AC: 1497 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	3.1
DANN	Benign	0.58
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs9972359; hg19: chr15-51491854;