2-60341610-A-T

Variant names:

• chr2-60341610-A-T
• rs243088
• ENST00000647917.1:n.1184T>A

Variant summary

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

The ENST00000647917.1(MIR4432HG):​n.1184T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 151,950 control chromosomes in the GnomAD database, including 19,467 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 0.50 (19467 hom., cov: 31)
• Consequence: MIR4432HG ENST00000647917.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.862
• Publications: 55 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.647 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	ENST00000647917.1	n.1184T>A		non_coding_transcript_exon_variant	Exon 1 of 4
MIR4432HG	ENST00000441598.2	n.1681+1207T>A		intron_variant	Intron 7 of 7	3
MIR4432HG	ENST00000730613.1	n.394-29592T>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76447 AN: 151832 Hom.: 19441 Cov.: 31

Gnomad AFR AF: 0.534

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.504 AC: 76516 AN: 151950 Hom.: 19467 Cov.: 31 AF XY: 0.504 AC XY: 37448 AN XY: 74250

African (AFR) AF: 0.534 AC: 22133 AN: 41426

American (AMR) AF: 0.573 AC: 8751 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1973 AN: 3468

East Asian (EAS) AF: 0.666 AC: 3431 AN: 5154

South Asian (SAS) AF: 0.512 AC: 2469 AN: 4820

European-Finnish (FIN) AF: 0.444 AC: 4676 AN: 10538

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.461 AC: 31312 AN: 67954

Other (OTH) AF: 0.540 AC: 1141 AN: 2114

Alfa AF: 0.484 Hom.: 2252

Bravo AF: 0.517

Asia WGS AF: 0.553 AC: 1924 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.15
DANN	Benign	0.45
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs243088; hg19: chr2-60568745;