rs5770418

Variant names:

• chr22-49418427-C-T
• rs5770418
• ENST00000414287.6:n.438-1499G>A

Variant summary

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

The ENST00000414287.6(MIR3667HG):​n.438-1499G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 152,040 control chromosomes in the GnomAD database, including 1,962 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 (1962 hom., cov: 32)
• Consequence: MIR3667HG ENST00000414287.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.20
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR3667HG	NR_110522.2	n.116-1499G>A		intron_variant	Intron 1 of 2
MIR3667HG	NR_110523.2	n.453-1499G>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR3667HG	ENST00000414287.6	n.438-1499G>A		intron_variant	Intron 2 of 4	1
MIR3667HG	ENST00000498829.1	n.368-1499G>A		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24423 AN: 151922 Hom.: 1950 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.161 AC: 24465 AN: 152040 Hom.: 1962 Cov.: 32 AF XY: 0.160 AC XY: 11894 AN XY: 74298

African (AFR) AF: 0.168 AC: 6964 AN: 41478

American (AMR) AF: 0.171 AC: 2606 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 625 AN: 3466

East Asian (EAS) AF: 0.133 AC: 686 AN: 5146

South Asian (SAS) AF: 0.139 AC: 670 AN: 4812

European-Finnish (FIN) AF: 0.136 AC: 1434 AN: 10566

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10790 AN: 67982

Other (OTH) AF: 0.166 AC: 349 AN: 2106

Alfa AF: 0.158 Hom.: 8253

Bravo AF: 0.163

Asia WGS AF: 0.178 AC: 620 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.72
DANN	Benign	0.89
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs5770418; hg19: chr22-49812076;