rs4927218

chr1-55283976-G-Achr1-55283976-G-C

Variant summary

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

The ENST00000643232.1(MIR4422HG):n.289-39002G>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 0.951 in 152,314 control chromosomes in the GnomAD database, including 68,888 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 0.95 (68888 hom., cov: 33)
• Consequence: MIR4422HG ENST00000643232.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.791

Genes affected

MIR4422HG (HGNC:53113): (MIR4422 host gene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.95 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR4422HG	ENST00000643232.1	n.289-39002G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.951 AC: 144737 AN: 152196 Hom.: 68837 Cov.: 33

Gnomad AFR AF: 0.958

Gnomad AMI AF: 0.992

Gnomad AMR AF: 0.962

Gnomad ASJ AF: 0.962

Gnomad EAS AF: 0.908

Gnomad SAS AF: 0.952

Gnomad FIN AF: 0.960

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.945

Gnomad OTH AF: 0.953

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

GnomAD4 genome AF: 0.951 AC: 144847 AN: 152314 Hom.: 68888 Cov.: 33 AF XY: 0.951 AC XY: 70814 AN XY: 74466

Gnomad4 AFR AF: 0.958

Gnomad4 AMR AF: 0.962

Gnomad4 ASJ AF: 0.962

Gnomad4 EAS AF: 0.909

Gnomad4 SAS AF: 0.951

Gnomad4 FIN AF: 0.960

Gnomad4 NFE AF: 0.945

Gnomad4 OTH AF: 0.952

Alfa AF: 0.945 Hom.: 15775

Bravo AF: 0.951

Asia WGS AF: 0.925 AC: 3217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	6.1
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4927218; hg19: chr1-55749649;