rs5770418

Positions:

• chr22-49418427-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.116-1499G>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 0.161 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 NR_110522.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.20

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=-0.93).
• 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/exons	MANE	UniProt
MIR3667HG	NR_110522.2	n.116-1499G>A		intron_variant, non_coding_transcript_variant
MIR3667HG	NR_110523.2	n.453-1499G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR3667HG	ENST00000414287.5	n.438-1499G>A		intron_variant, non_coding_transcript_variant		1
MIR3667HG	ENST00000498829.1	n.368-1499G>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.168

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.180

Gnomad4 EAS AF: 0.133

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.166

Alfa AF: 0.159 Hom.: 4097

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5770418; hg19: chr22-49812076;