chr2-60356592-T-C

Variant names:

• chr2-60356592-T-C
• rs243023
• ENST00000441598.2:n.920+2678A>G

Variant summary

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

The ENST00000441598.2(MIR4432HG):​n.920+2678A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.935 in 152,042 control chromosomes in the GnomAD database, including 66,569 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 0.94 (66569 hom., cov: 28)
• Consequence: MIR4432HG ENST00000441598.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.828
• Publications: 3 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 (EAS) allele frequency at 95% confidence interval = 0.975 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR4432HG	ENST00000441598.2	TSL:3	n.920+2678A>G		intron	N/A
	MIR4432HG	ENST00000730613.1		n.394-44574A>G		intron	N/A
	MIR4432HG	ENST00000730614.1		n.373-44574A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.935 AC: 142052 AN: 151924 Hom.: 66504 Cov.: 28

Gnomad AFR AF: 0.983

Gnomad AMI AF: 0.917

Gnomad AMR AF: 0.938

Gnomad ASJ AF: 0.912

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.958

Gnomad FIN AF: 0.951

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.898

Gnomad OTH AF: 0.928

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

GnomAD4 genome AF: 0.935 AC: 142176 AN: 152042 Hom.: 66569 Cov.: 28 AF XY: 0.938 AC XY: 69751 AN XY: 74322

African (AFR) AF: 0.983 AC: 40720 AN: 41428

American (AMR) AF: 0.938 AC: 14320 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.912 AC: 3166 AN: 3472

East Asian (EAS) AF: 0.996 AC: 5138 AN: 5160

South Asian (SAS) AF: 0.958 AC: 4605 AN: 4808

European-Finnish (FIN) AF: 0.951 AC: 10072 AN: 10592

Middle Eastern (MID) AF: 0.888 AC: 261 AN: 294

European-Non Finnish (NFE) AF: 0.899 AC: 61093 AN: 67992

Other (OTH) AF: 0.930 AC: 1965 AN: 2114

Alfa AF: 0.910 Hom.: 26277

Bravo AF: 0.935

Asia WGS AF: 0.970 AC: 3375 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	0.98
DANN	Benign	0.71
PhyloP100		-0.83

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs243023; hg19: chr2-60583727;