ENST00000650395.1:n.265+6391A>G

Variant names:

• chr2-60433173-T-C
• rs17402905
• XM_047446573.1:c.331+6099A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000650395.1(MIR4432HG):​n.265+6391A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 152,108 control chromosomes in the GnomAD database, including 4,093 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 0.22 (4093 hom., cov: 32)
• Consequence: MIR4432HG ENST00000650395.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0620
• Publications: 9 publications found

Genes affected

LOC124906010 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650395.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR4432HG	ENST00000650395.1		n.265+6391A>G		intron	N/A
	MIR4432HG	ENST00000730613.1		n.270+6391A>G		intron	N/A
	MIR4432HG	ENST00000730614.1		n.253+6391A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.217 AC: 33043 AN: 151990 Hom.: 4096 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.00424

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.217 AC: 33035 AN: 152108 Hom.: 4093 Cov.: 32 AF XY: 0.212 AC XY: 15750 AN XY: 74352

African (AFR) AF: 0.145 AC: 6033 AN: 41492

American (AMR) AF: 0.161 AC: 2466 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 592 AN: 3468

East Asian (EAS) AF: 0.00425 AC: 22 AN: 5182

South Asian (SAS) AF: 0.122 AC: 587 AN: 4820

European-Finnish (FIN) AF: 0.299 AC: 3158 AN: 10568

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.285 AC: 19354 AN: 67974

Other (OTH) AF: 0.180 AC: 380 AN: 2110

Alfa AF: 0.200 Hom.: 1434

Bravo AF: 0.204

Asia WGS AF: 0.0610 AC: 214 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.1
DANN	Benign	0.37
PhyloP100		0.062

Splicing

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

Other links and lift over

dbSNP: rs17402905; hg19: chr2-60660308;