rs9627735

Variant names:

• chr22-49448640-A-T
• rs9627735
• ENST00000414287.6:n.101-7428T>A

Variant summary

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

The ENST00000414287.6(MIR3667HG):​n.101-7428T>A variant causes a intron change. The variant allele was found at a frequency of 0.176 in 152,202 control chromosomes in the GnomAD database, including 2,627 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 0.18 (2627 hom., cov: 33)
• Consequence: MIR3667HG ENST00000414287.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.55
• Publications: 5 publications found

Genes affected

MIR3667HG (HGNC:28010): (MIR3667 host gene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000414287.6. 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
	MIR3667HG	NR_110522.2		n.116-31712T>A		intron	N/A
	MIR3667HG	NR_110523.2		n.116-7428T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR3667HG	ENST00000414287.6	TSL:1	n.101-7428T>A		intron	N/A
	MIR3667HG	ENST00000416411.1	TSL:4	n.54-7428T>A		intron	N/A
	MIR3667HG	ENST00000794975.1		n.111+1554T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26836 AN: 152082 Hom.: 2627 Cov.: 33

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.0473

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.176 AC: 26841 AN: 152202 Hom.: 2627 Cov.: 33 AF XY: 0.173 AC XY: 12841 AN XY: 74422

African (AFR) AF: 0.120 AC: 4987 AN: 41502

American (AMR) AF: 0.168 AC: 2569 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 865 AN: 3470

East Asian (EAS) AF: 0.0470 AC: 244 AN: 5194

South Asian (SAS) AF: 0.179 AC: 866 AN: 4828

European-Finnish (FIN) AF: 0.152 AC: 1612 AN: 10612

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.221 AC: 15011 AN: 67982

Other (OTH) AF: 0.206 AC: 436 AN: 2112

Alfa AF: 0.181 Hom.: 311

Bravo AF: 0.175

Asia WGS AF: 0.0980 AC: 343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	13
DANN	Benign	0.74
PhyloP100		4.5

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: rs9627735;

hg19: chr22-49842289;