22-49545661-C-T

Variant names:

• chr22-49545661-C-T
• rs135775
• ENST00000414287.6:n.101-104449G>A

Variant summary

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

The ENST00000414287.6(MIR3667HG):​n.101-104449G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 151,804 control chromosomes in the GnomAD database, including 2,512 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 0.16 (2512 hom., cov: 31)
• Consequence: MIR3667HG ENST00000414287.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.66
• Publications: 4 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=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR3667HG	NR_110522.2	n.115+111744G>A		intron_variant	Intron 1 of 2
MIR3667HG	NR_110523.2	n.116-104449G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR3667HG	ENST00000414287.6	n.101-104449G>A		intron_variant	Intron 1 of 4	1
MIR3667HG	ENST00000416411.1	n.54-104449G>A		intron_variant	Intron 1 of 2	4
MIR3667HG	ENST00000752354.1	n.116-55409G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24572 AN: 151690 Hom.: 2509 Cov.: 31

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0559

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.162 AC: 24604 AN: 151804 Hom.: 2512 Cov.: 31 AF XY: 0.160 AC XY: 11863 AN XY: 74190

African (AFR) AF: 0.274 AC: 11340 AN: 41318

American (AMR) AF: 0.111 AC: 1696 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 645 AN: 3468

East Asian (EAS) AF: 0.306 AC: 1571 AN: 5130

South Asian (SAS) AF: 0.114 AC: 549 AN: 4816

European-Finnish (FIN) AF: 0.0559 AC: 589 AN: 10542

Middle Eastern (MID) AF: 0.144 AC: 42 AN: 292

European-Non Finnish (NFE) AF: 0.114 AC: 7744 AN: 67940

Other (OTH) AF: 0.154 AC: 325 AN: 2108

Alfa AF: 0.136 Hom.: 4662

Bravo AF: 0.175

Asia WGS AF: 0.208 AC: 724 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.10
DANN	Benign	0.39
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs135775; hg19: chr22-49939309;