rs9300547

Positions:

• chr13-87577000-C-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_033829.1(MIR4500HG):​n.129-65530G>C 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 0.355 in 151,798 control chromosomes in the GnomAD database, including 9,995 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 0.35 (9995 hom., cov: 32)
• Consequence: MIR4500HG NR_033829.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206

Genes affected

MIR4500HG (HGNC:42773): (MIR4500 host gene)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.26).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR4500HG	NR_033829.1	n.129-65530G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR4500HG	ENST00000436290.2	n.129-65530G>C		intron_variant, non_coding_transcript_variant		1
MIR4500HG	ENST00000656150.1	n.656-16583G>C		intron_variant, non_coding_transcript_variant
MIR4500HG	ENST00000658487.1	n.682+38563G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53797 AN: 151680 Hom.: 9984 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.355 AC: 53837 AN: 151798 Hom.: 9995 Cov.: 32 AF XY: 0.359 AC XY: 26663 AN XY: 74182

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.467

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.442

Gnomad4 SAS AF: 0.389

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.365

Alfa AF: 0.373 Hom.: 1351

Bravo AF: 0.353

Asia WGS AF: 0.433 AC: 1502 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
CADD	Benign	16
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9300547; hg19: chr13-88229255;