rs243030

chr2-60379436-C-T

Variant summary

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

The NR_132992.1(MIR4432HG):n.70+11870G>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 0.327 in 151,862 control chromosomes in the GnomAD database, including 8,811 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 0.33 (8811 hom., cov: 31)
• Consequence: MIR4432HG NR_132992.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.362

Genes affected

MIR4432HG (HGNC:52005): (MIR4432 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 (NFE) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR4432HG	NR_132992.1	n.70+11870G>A		intron_variant, non_coding_transcript_variant
MIR4432HG	NR_132991.1	n.94-816G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR4432HG	ENST00000650395.1	n.389-9399G>A		intron_variant, non_coding_transcript_variant
MIR4432HG	ENST00000441598.2	n.94-816G>A		intron_variant, non_coding_transcript_variant		3
MIR4432HG	ENST00000453476.1	n.70+11870G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49636 AN: 151744 Hom.: 8812 Cov.: 31

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.00596

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.327 AC: 49650 AN: 151862 Hom.: 8811 Cov.: 31 AF XY: 0.318 AC XY: 23559 AN XY: 74188

Gnomad4 AFR AF: 0.290

Gnomad4 AMR AF: 0.244

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.00617

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.394

Gnomad4 NFE AF: 0.397

Gnomad4 OTH AF: 0.288

Alfa AF: 0.347 Hom.: 2812

Bravo AF: 0.314

Asia WGS AF: 0.0910 AC: 315 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	2.0
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs243030; hg19: chr2-60606571;