rs7167936

Variant names:

• chr15-51207348-A-G
• rs7167936
• ENST00000559909.1:n.195-70635A>G

Variant summary

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

The ENST00000559909.1(MIR4713HG):​n.195-70635A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 152,094 control chromosomes in the GnomAD database, including 15,170 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 0.43 (15170 hom., cov: 32)
• Consequence: MIR4713HG ENST00000559909.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR4713HG	NR_146310.1	n.195-70635A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR4713HG	ENST00000559909.1	n.195-70635A>G		intron_variant	Intron 1 of 2	4
MIR4713HG	ENST00000805692.1	n.279-70635A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65345 AN: 151976 Hom.: 15167 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.430 AC: 65367 AN: 152094 Hom.: 15170 Cov.: 32 AF XY: 0.428 AC XY: 31787 AN XY: 74348

African (AFR) AF: 0.250 AC: 10361 AN: 41496

American (AMR) AF: 0.374 AC: 5715 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.565 AC: 1961 AN: 3470

East Asian (EAS) AF: 0.498 AC: 2568 AN: 5160

South Asian (SAS) AF: 0.365 AC: 1760 AN: 4824

European-Finnish (FIN) AF: 0.523 AC: 5530 AN: 10574

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.528 AC: 35921 AN: 67980

Other (OTH) AF: 0.450 AC: 952 AN: 2116

Alfa AF: 0.474 Hom.: 2817

Bravo AF: 0.415

Asia WGS AF: 0.380 AC: 1322 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.13
DANN	Benign	0.42
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs7167936; hg19: chr15-51499545;