rs9947662

Positions:

• chr18-47333893-G-A
• chr18-47333893-G-C

Variant summary

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

The NR_147192.1(MIR4527HG):​n.38+48132G>A 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 0.252 in 152,184 control chromosomes in the GnomAD database, including 4,964 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 0.25 (4964 hom., cov: 33)
• Consequence: MIR4527HG NR_147192.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.615

Genes affected

MIR4527HG (HGNC:31724): (MIR4527 host gene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.362 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR4527HG	NR_147192.1	n.38+48132G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR4527HG	ENST00000586905.3	n.37+48132G>A		intron_variant, non_coding_transcript_variant		1
MIR4527HG	ENST00000598649.1	n.73+48096G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38280 AN: 152066 Hom.: 4955 Cov.: 33

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.252 AC: 38306 AN: 152184 Hom.: 4964 Cov.: 33 AF XY: 0.256 AC XY: 19037 AN XY: 74398

Gnomad4 AFR AF: 0.233

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.269

Gnomad4 EAS AF: 0.253

Gnomad4 SAS AF: 0.377

Gnomad4 FIN AF: 0.267

Gnomad4 NFE AF: 0.263

Gnomad4 OTH AF: 0.228

Alfa AF: 0.252 Hom.: 611

Bravo AF: 0.240

Asia WGS AF: 0.262 AC: 914 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.1
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9947662; hg19: chr18-44860264;