chr2-60393151-T-A

Position:

• chr2-60393151-T-A

Variant summary

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

The ENST00000650395.1(MIR4432HG):​n.388+8937A>T 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 0.207 in 152,196 control chromosomes in the GnomAD database, including 3,899 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 0.21 (3899 hom., cov: 33)
• Consequence: MIR4432HG ENST00000650395.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.126

Genes affected

MIR4432HG (HGNC:52005): (MIR4432 host gene)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.29).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.282 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	ENST00000650395.1	n.388+8937A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31467 AN: 152078 Hom.: 3902 Cov.: 33

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.00404

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.207 AC: 31461 AN: 152196 Hom.: 3899 Cov.: 33 AF XY: 0.202 AC XY: 15069 AN XY: 74418

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.155

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.00405

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.285

Gnomad4 OTH AF: 0.170

Alfa AF: 0.246 Hom.: 615

Bravo AF: 0.191

Asia WGS AF: 0.0560 AC: 196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
CADD	Benign	9.9
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs243070; hg19: chr2-60620286;