chr2-60375757-C-T

Variant names:

• chr2-60375757-C-T
• rs243034
• ENST00000441598.2:n.212+2745G>A

Variant summary

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

The ENST00000441598.2(MIR4432HG):​n.212+2745G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.568 in 151,912 control chromosomes in the GnomAD database, including 25,136 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 0.57 (25136 hom., cov: 31)
• Consequence: MIR4432HG ENST00000441598.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.383
• Publications: 7 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.606 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.212+2745G>A		intron	N/A
	MIR4432HG	NR_132992.1		n.70+15549G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR4432HG	ENST00000441598.2	TSL:3	n.212+2745G>A		intron	N/A
	MIR4432HG	ENST00000453476.1	TSL:3	n.70+15549G>A		intron	N/A
	MIR4432HG	ENST00000650395.1		n.389-5720G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86284 AN: 151794 Hom.: 25114 Cov.: 31

Gnomad AFR AF: 0.569

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.568 AC: 86358 AN: 151912 Hom.: 25136 Cov.: 31 AF XY: 0.562 AC XY: 41728 AN XY: 74254

African (AFR) AF: 0.569 AC: 23559 AN: 41414

American (AMR) AF: 0.477 AC: 7288 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.525 AC: 1818 AN: 3466

East Asian (EAS) AF: 0.252 AC: 1303 AN: 5168

South Asian (SAS) AF: 0.438 AC: 2101 AN: 4792

European-Finnish (FIN) AF: 0.644 AC: 6791 AN: 10546

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.611 AC: 41545 AN: 67954

Other (OTH) AF: 0.566 AC: 1191 AN: 2106

Alfa AF: 0.587 Hom.: 53440

Bravo AF: 0.554

Asia WGS AF: 0.398 AC: 1381 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.8
DANN	Benign	0.74
PhyloP100		0.38

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: rs243034;

hg19: chr2-60602892;