22-49640829-C-T

Variant names:

• chr22-49640829-C-T
• rs2071904
• ENST00000400023.5:n.139-15893G>A

Variant summary

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

The ENST00000400023.5(MIR3667HG):​n.139-15893G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.496 in 151,840 control chromosomes in the GnomAD database, including 21,060 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 0.50 (21060 hom., cov: 31)
• Consequence: MIR3667HG ENST00000400023.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 14 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000400023.5. 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.115+16576G>A		intron	N/A
	MIR3667HG	NR_110523.2		n.115+16576G>A		intron	N/A
	MIR3667HG	NR_171025.1		n.116-15893G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR3667HG	ENST00000400023.5	TSL:1	n.139-15893G>A		intron	N/A
	MIR3667HG	ENST00000414287.6	TSL:1	n.100+16576G>A		intron	N/A
	MIR3667HG	ENST00000405854.5	TSL:5	n.808-13782G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75257 AN: 151722 Hom.: 21054 Cov.: 31

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.524

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.496 AC: 75281 AN: 151840 Hom.: 21060 Cov.: 31 AF XY: 0.496 AC XY: 36778 AN XY: 74200

African (AFR) AF: 0.235 AC: 9735 AN: 41434

American (AMR) AF: 0.673 AC: 10274 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.524 AC: 1817 AN: 3466

East Asian (EAS) AF: 0.359 AC: 1844 AN: 5136

South Asian (SAS) AF: 0.488 AC: 2344 AN: 4806

European-Finnish (FIN) AF: 0.612 AC: 6444 AN: 10536

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.608 AC: 41287 AN: 67886

Other (OTH) AF: 0.525 AC: 1106 AN: 2108

Alfa AF: 0.571 Hom.: 12569

Bravo AF: 0.487

Asia WGS AF: 0.401 AC: 1392 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.0
DANN	Benign	0.47
PhyloP100		-1.2
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

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: rs2071904;

hg19: chr22-50034477;