ENST00000441598.2:n.920+2678A>G

Variant names:

• chr2-60356592-T-C
• rs243023
• ENST00000441598.2:n.920+2678A>G

Variant summary

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

The ENST00000441598.2(MIR4432HG):​n.920+2678A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.935 in 152,042 control chromosomes in the GnomAD database, including 66,569 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 0.94 (66569 hom., cov: 28)
• Consequence: MIR4432HG ENST00000441598.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.828

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR4432HG	ENST00000441598.2	n.920+2678A>G		intron_variant	Intron 4 of 7	3

Frequencies

GnomAD3 genomes AF: 0.935 AC: 142052 AN: 151924 Hom.: 66504 Cov.: 28

Gnomad AFR AF: 0.983

Gnomad AMI AF: 0.917

Gnomad AMR AF: 0.938

Gnomad ASJ AF: 0.912

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.958

Gnomad FIN AF: 0.951

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.898

Gnomad OTH AF: 0.928

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

GnomAD4 genome AF: 0.935 AC: 142176 AN: 152042 Hom.: 66569 Cov.: 28 AF XY: 0.938 AC XY: 69751 AN XY: 74322

Gnomad4 AFR AF: 0.983

Gnomad4 AMR AF: 0.938

Gnomad4 ASJ AF: 0.912

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.958

Gnomad4 FIN AF: 0.951

Gnomad4 NFE AF: 0.899

Gnomad4 OTH AF: 0.930

Alfa AF: 0.910 Hom.: 22780

Bravo AF: 0.935

Asia WGS AF: 0.970 AC: 3375 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	0.98
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs243023; hg19: chr2-60583727;