rs11894442

Variant names:

• chr2-60429883-T-C
• rs11894442
• XM_047446573.1:c.331+9389A>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+9681A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.509 in 151,972 control chromosomes in the GnomAD database, including 20,097 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 0.51 (20097 hom., cov: 32)
• Consequence: MIR4432HG ENST00000650395.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 6 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.649 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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR4432HG	ENST00000650395.1		n.265+9681A>G		intron	N/A
	MIR4432HG	ENST00000730613.1		n.270+9681A>G		intron	N/A
	MIR4432HG	ENST00000730614.1		n.253+9681A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77315 AN: 151852 Hom.: 20069 Cov.: 32

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.509 AC: 77393 AN: 151972 Hom.: 20097 Cov.: 32 AF XY: 0.511 AC XY: 37963 AN XY: 74274

African (AFR) AF: 0.541 AC: 22410 AN: 41422

American (AMR) AF: 0.542 AC: 8270 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1031 AN: 3470

East Asian (EAS) AF: 0.667 AC: 3452 AN: 5172

South Asian (SAS) AF: 0.497 AC: 2391 AN: 4808

European-Finnish (FIN) AF: 0.556 AC: 5872 AN: 10552

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.477 AC: 32431 AN: 67966

Other (OTH) AF: 0.457 AC: 962 AN: 2106

Alfa AF: 0.482 Hom.: 9420

Bravo AF: 0.512

Asia WGS AF: 0.564 AC: 1957 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.36
DANN	Benign	0.24
PhyloP100		-1.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11894442;

hg19: chr2-60657018;