2-60438633-A-G

Variant names:

• chr2-60438633-A-G
• rs1011407
• ENST00000730654.1:n.1070T>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

MIR4432HG (HGNC:52005): (MIR4432 host gene)

LOC124906010 (HGNC:):

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124906010	XM_047446573.1	c.331+639T>C		intron_variant	Intron 2 of 2		XP_047302529.1
LOC124906010	XM_047446574.1	c.331+639T>C		intron_variant	Intron 2 of 2		XP_047302530.1
LOC124906010	XR_007086328.1	n.422+639T>C		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR4432HG	ENST00000730654.1	n.1070T>C		non_coding_transcript_exon_variant	Exon 2 of 2
MIR4432HG	ENST00000650395.1	n.265+931T>C		intron_variant	Intron 1 of 3
MIR4432HG	ENST00000686152.2	n.266-919T>C		intron_variant	Intron 1 of 1

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 v4.3

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

Other links and lift over

dbSNP: rs1011407; hg19: chr2-60665768;