chr2-60436663-C-T

Variant names:

• chr2-60436663-C-T
• rs8179712
• ENST00000650395.1:n.265+2901G>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

MIR4432HG (HGNC:52005): (MIR4432 host gene)

LOC124906010 (HGNC:):

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124906010	XM_047446573.1	c.331+2609G>A		intron_variant	Intron 2 of 2		XP_047302529.1
LOC124906010	XR_007086328.1	n.497+977G>A		intron_variant	Intron 3 of 5
LOC124906010	XR_007086329.1	n.422+2609G>A		intron_variant	Intron 2 of 4
LOC124906010	XR_007086331.1	n.256+2901G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR4432HG	ENST00000650395.1	n.265+2901G>A		intron_variant	Intron 1 of 3
MIR4432HG	ENST00000730613.1	n.270+2901G>A		intron_variant	Intron 1 of 2
MIR4432HG	ENST00000730614.1	n.253+2901G>A		intron_variant	Intron 1 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs8179712; hg19: chr2-60663798;