rs30222

Variant names:

• chr16-14315801-G-A
• rs30222
• ENST00000570945.2:n.293-10212G>A

Variant summary

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

The ENST00000570945.2(MIR193BHG):​n.293-10212G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.72 in 152,208 control chromosomes in the GnomAD database, including 40,827 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 0.72 (40827 hom., cov: 33)
• Consequence: MIR193BHG ENST00000570945.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80
• Publications: 2 publications found

Genes affected

MIR193BHG (HGNC:51945): (MIR193b-365a host gene)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.911 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000570945.2. 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
	MIR193BHG	NR_132983.2		n.355-10212G>A		intron	N/A
	MIR193BHG	NR_132984.2		n.294-10212G>A		intron	N/A
	MIR193BHG	NR_170633.1		n.152-10212G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR193BHG	ENST00000570945.2	TSL:3	n.293-10212G>A		intron	N/A
	MIR193BHG	ENST00000634265.3	TSL:5	n.419-10212G>A		intron	N/A
	MIR193BHG	ENST00000641175.1		n.122-10212G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.720 AC: 109508 AN: 152090 Hom.: 40768 Cov.: 33

Gnomad AFR AF: 0.919

Gnomad AMI AF: 0.574

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.643

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.723

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

GnomAD4 genome AF: 0.720 AC: 109629 AN: 152208 Hom.: 40827 Cov.: 33 AF XY: 0.720 AC XY: 53557 AN XY: 74396

African (AFR) AF: 0.919 AC: 38200 AN: 41578

American (AMR) AF: 0.650 AC: 9942 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.643 AC: 2230 AN: 3468

East Asian (EAS) AF: 0.765 AC: 3963 AN: 5182

South Asian (SAS) AF: 0.690 AC: 3327 AN: 4822

European-Finnish (FIN) AF: 0.626 AC: 6619 AN: 10566

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.634 AC: 43074 AN: 67992

Other (OTH) AF: 0.727 AC: 1534 AN: 2110

Alfa AF: 0.689 Hom.: 12980

Bravo AF: 0.727

Asia WGS AF: 0.751 AC: 2612 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.12
DANN	Benign	0.56
PhyloP100		-1.8

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: rs30222;

hg19: chr16-14409658;