rs9627735

chr22-49448640-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_110522.2(MIR3667HG):n.116-31712T>A variant causes a intron, non coding transcript 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 NR_110522.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.55

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR3667HG	NR_110522.2	n.116-31712T>A		intron_variant, non_coding_transcript_variant
MIR3667HG	NR_110523.2	n.116-7428T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR3667HG	ENST00000414287.5	n.101-7428T>A		intron_variant, non_coding_transcript_variant		1
MIR3667HG	ENST00000416411.1	n.54-7428T>A		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.0470

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.221

Gnomad4 OTH AF: 0.206

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
Cadd	Benign	13
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9627735; hg19: chr22-49842289;