chr2-60356592-T-C

Position:

• chr2-60356592-T-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR4432HG	ENST00000441598.2	n.920+2678A>G		intron_variant		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;