22-49545661-C-T

Position:

• chr22-49545661-C-T

Variant summary

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

The NR_110522.2(MIR3667HG):​n.115+111744G>A variant causes a intron, non coding transcript 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 NR_110522.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.66

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=-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/exons	MANE	UniProt
MIR3667HG	NR_110522.2	n.115+111744G>A		intron_variant, non_coding_transcript_variant
MIR3667HG	NR_110523.2	n.116-104449G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR3667HG	ENST00000414287.5	n.101-104449G>A		intron_variant, non_coding_transcript_variant		1
MIR3667HG	ENST00000416411.1	n.54-104449G>A		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.274

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.306

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.0559

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.154

Alfa AF: 0.127 Hom.: 1435

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs135775; hg19: chr22-49939309;