rs6718203

Variant names:

• chr2-60432172-C-G
• rs6718203
• XM_047446573.1:c.331+7100G>C

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4 BA1

The ENST00000650395.1(MIR4432HG):​n.265+7392G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 151,804 control chromosomes in the GnomAD database, including 1,162 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 0.12 (1162 hom., cov: 31)
• Consequence: MIR4432HG ENST00000650395.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.786
• Publications: 4 publications found

Genes affected

LOC124906010 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.14).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650395.1. 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	ENST00000650395.1		n.265+7392G>C		intron	N/A
	MIR4432HG	ENST00000730613.1		n.270+7392G>C		intron	N/A
	MIR4432HG	ENST00000730614.1		n.253+7392G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17588 AN: 151686 Hom.: 1161 Cov.: 31

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.0884

Gnomad ASJ AF: 0.0869

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0372

Gnomad FIN AF: 0.0781

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.116 AC: 17604 AN: 151804 Hom.: 1162 Cov.: 31 AF XY: 0.112 AC XY: 8300 AN XY: 74184

African (AFR) AF: 0.161 AC: 6668 AN: 41344

American (AMR) AF: 0.0882 AC: 1346 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0869 AC: 301 AN: 3464

East Asian (EAS) AF: 0.00193 AC: 10 AN: 5178

South Asian (SAS) AF: 0.0374 AC: 180 AN: 4814

European-Finnish (FIN) AF: 0.0781 AC: 820 AN: 10500

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7950 AN: 67946

Other (OTH) AF: 0.105 AC: 221 AN: 2098

Alfa AF: 0.113 Hom.: 120

Bravo AF: 0.119

Asia WGS AF: 0.0300 AC: 105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.14
CADD	Benign	17
DANN	Benign	0.68
PhyloP100		0.79

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: rs6718203;

hg19: chr2-60659307;