2-60381624-T-C

Variant names:

• chr2-60381624-T-C
• rs2540917
• ENST00000441598.2:n.93+1320A>G

Variant summary

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

The ENST00000441598.2(MIR4432HG):​n.93+1320A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 152,144 control chromosomes in the GnomAD database, including 7,394 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 0.28 (7394 hom., cov: 33)
• Consequence: MIR4432HG ENST00000441598.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.683
• Publications: 32 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.392 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.93+1320A>G		intron	N/A
	MIR4432HG	NR_132992.1		n.70+9682A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR4432HG	ENST00000441598.2	TSL:3	n.93+1320A>G		intron	N/A
	MIR4432HG	ENST00000453476.1	TSL:3	n.70+9682A>G		intron	N/A
	MIR4432HG	ENST00000650395.1		n.389-11587A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43148 AN: 152026 Hom.: 7400 Cov.: 33

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.00577

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.284 AC: 43138 AN: 152144 Hom.: 7394 Cov.: 33 AF XY: 0.276 AC XY: 20509 AN XY: 74372

African (AFR) AF: 0.139 AC: 5783 AN: 41512

American (AMR) AF: 0.229 AC: 3506 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 891 AN: 3470

East Asian (EAS) AF: 0.00598 AC: 31 AN: 5186

South Asian (SAS) AF: 0.154 AC: 741 AN: 4826

European-Finnish (FIN) AF: 0.394 AC: 4161 AN: 10570

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.396 AC: 26931 AN: 67978

Other (OTH) AF: 0.261 AC: 552 AN: 2112

Alfa AF: 0.353 Hom.: 29817

Bravo AF: 0.266

Asia WGS AF: 0.0800 AC: 278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.5
DANN	Benign	0.62
PhyloP100		0.68

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: rs2540917;

hg19: chr2-60608759;