2-60436663-C-T

Variant names:

• chr2-60436663-C-T
• rs8179712
• XM_047446573.1:c.331+2609G>A

Variant summary

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

The ENST00000650395.1(MIR4432HG):​n.265+2901G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,144 control chromosomes in the GnomAD database, including 2,841 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 0.14 (2841 hom., cov: 32)
• Consequence: MIR4432HG ENST00000650395.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.413
• Publications: 4 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.636 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+2901G>A		intron	N/A
	MIR4432HG	ENST00000730613.1		n.270+2901G>A		intron	N/A
	MIR4432HG	ENST00000730614.1		n.253+2901G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22029 AN: 152026 Hom.: 2830 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.0386

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0713

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.145 AC: 22059 AN: 152144 Hom.: 2841 Cov.: 32 AF XY: 0.159 AC XY: 11790 AN XY: 74382

African (AFR) AF: 0.141 AC: 5850 AN: 41506

American (AMR) AF: 0.273 AC: 4171 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0386 AC: 134 AN: 3470

East Asian (EAS) AF: 0.654 AC: 3380 AN: 5168

South Asian (SAS) AF: 0.334 AC: 1608 AN: 4816

European-Finnish (FIN) AF: 0.167 AC: 1771 AN: 10580

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0713 AC: 4849 AN: 68010

Other (OTH) AF: 0.129 AC: 272 AN: 2110

Alfa AF: 0.0984 Hom.: 2137

Bravo AF: 0.155

Asia WGS AF: 0.460 AC: 1596 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.4
DANN	Benign	0.68
PhyloP100		0.41

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: rs8179712;

hg19: chr2-60663798;