2-60358671-T-C

Variant names:

• chr2-60358671-T-C
• rs243019
• ENST00000441598.2:n.920+599A>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+599A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 152,068 control chromosomes in the GnomAD database, including 16,542 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 0.46 (16542 hom., cov: 32)
• Consequence: MIR4432HG ENST00000441598.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.411
• Publications: 20 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=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR4432HG	ENST00000441598.2	n.920+599A>G		intron_variant	Intron 4 of 7	3
MIR4432HG	ENST00000730613.1	n.393+43417A>G		intron_variant	Intron 2 of 2
MIR4432HG	ENST00000730614.1	n.372+43417A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70406 AN: 151950 Hom.: 16538 Cov.: 32

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.669

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.463 AC: 70431 AN: 152068 Hom.: 16542 Cov.: 32 AF XY: 0.465 AC XY: 34572 AN XY: 74334

African (AFR) AF: 0.399 AC: 16553 AN: 41472

American (AMR) AF: 0.553 AC: 8449 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1875 AN: 3464

East Asian (EAS) AF: 0.669 AC: 3462 AN: 5174

South Asian (SAS) AF: 0.507 AC: 2445 AN: 4820

European-Finnish (FIN) AF: 0.436 AC: 4598 AN: 10552

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.463 AC: 31458 AN: 67980

Other (OTH) AF: 0.509 AC: 1076 AN: 2112

Alfa AF: 0.472 Hom.: 2823

Bravo AF: 0.471

Asia WGS AF: 0.536 AC: 1865 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	6.4
DANN	Benign	0.64
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs243019; hg19: chr2-60585806;