2-60361578-A-T

Variant names:

• chr2-60361578-A-T
• rs243016
• ENST00000441598.2:n.342-1730T>A

Variant summary

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

The ENST00000441598.2(MIR4432HG):​n.342-1730T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 152,186 control chromosomes in the GnomAD database, including 5,323 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 0.24 (5323 hom., cov: 33)
• Consequence: MIR4432HG ENST00000441598.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10
• Publications: 6 publications found

Genes affected

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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000441598.2. 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
	MIR4432HG	NR_132991.1		n.342-1730T>A		intron	N/A
	MIR4432HG	NR_132992.1		n.71-1730T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR4432HG	ENST00000441598.2	TSL:3	n.342-1730T>A		intron	N/A
	MIR4432HG	ENST00000453476.1	TSL:3	n.71-1730T>A		intron	N/A
	MIR4432HG	ENST00000650395.1		n.518-1730T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36340 AN: 152068 Hom.: 5325 Cov.: 33

Gnomad AFR AF: 0.0919

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.239 AC: 36363 AN: 152186 Hom.: 5323 Cov.: 33 AF XY: 0.239 AC XY: 17775 AN XY: 74398

African (AFR) AF: 0.0920 AC: 3821 AN: 41554

American (AMR) AF: 0.210 AC: 3207 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 638 AN: 3470

East Asian (EAS) AF: 0.105 AC: 545 AN: 5188

South Asian (SAS) AF: 0.114 AC: 551 AN: 4828

European-Finnish (FIN) AF: 0.430 AC: 4540 AN: 10566

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.329 AC: 22351 AN: 67972

Other (OTH) AF: 0.208 AC: 440 AN: 2112

Alfa AF: 0.292 Hom.: 905

Bravo AF: 0.219

Asia WGS AF: 0.0990 AC: 343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.1
DANN	Benign	0.70
PhyloP100		1.1

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: rs243016;

hg19: chr2-60588713;