rs1011407

Variant names:

• chr2-60438633-A-G
• rs1011407
• XM_047446573.1:c.331+639T>C

Variant summary

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

The ENST00000730654.1(MIR4432HG):​n.1070T>C 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 0.0759 in 152,330 control chromosomes in the GnomAD database, including 593 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 0.076 (593 hom., cov: 32)
• Consequence: MIR4432HG ENST00000730654.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0940
• Publications: 10 publications found

Genes affected

LOC124906010 (HGNC:):

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000730654.1. 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	ENST00000730654.1		n.1070T>C		non_coding_transcript_exon	Exon 2 of 2
	MIR4432HG	ENST00000650395.1		n.265+931T>C		intron	N/A
	MIR4432HG	ENST00000686152.2		n.266-919T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0760 AC: 11573 AN: 152212 Hom.: 592 Cov.: 32

Gnomad AFR AF: 0.0210

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.0769

Gnomad ASJ AF: 0.0867

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0360

Gnomad FIN AF: 0.0778

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.0919

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

GnomAD4 genome AF: 0.0759 AC: 11569 AN: 152330 Hom.: 593 Cov.: 32 AF XY: 0.0727 AC XY: 5414 AN XY: 74492

African (AFR) AF: 0.0209 AC: 869 AN: 41568

American (AMR) AF: 0.0768 AC: 1176 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0867 AC: 301 AN: 3472

East Asian (EAS) AF: 0.00193 AC: 10 AN: 5194

South Asian (SAS) AF: 0.0362 AC: 175 AN: 4832

European-Finnish (FIN) AF: 0.0778 AC: 826 AN: 10620

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7922 AN: 68022

Other (OTH) AF: 0.0895 AC: 189 AN: 2112

Alfa AF: 0.105 Hom.: 463

Bravo AF: 0.0742

Asia WGS AF: 0.0210 AC: 72 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.6
DANN	Benign	0.38
PhyloP100		-0.094

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1011407;

hg19: chr2-60665768;