2-60341610-A-T

Position:

• chr2-60341610-A-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

MIR4432HG (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.60341610A>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR4432HG	ENST00000647917.1	n.1184T>A		non_coding_transcript_exon_variant	1/4
MIR4432HG	ENST00000441598.2	n.1681+1207T>A		intron_variant		3

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

Gnomad4 AFR AF: 0.534

Gnomad4 AMR AF: 0.573

Gnomad4 ASJ AF: 0.569

Gnomad4 EAS AF: 0.666

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.444

Gnomad4 NFE AF: 0.461

Gnomad4 OTH AF: 0.540

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs243088; hg19: chr2-60568745;