1-55315148-C-T

Variant names:

• chr1-55315148-C-T
• rs1807871
• ENST00000643232.1:n.289-7830C>T

Variant summary

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

The ENST00000643232.1(MIR4422HG):​n.289-7830C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.739 in 152,136 control chromosomes in the GnomAD database, including 44,126 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 0.74 (44126 hom., cov: 33)
• Consequence: MIR4422HG ENST00000643232.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.137
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.864 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR4422HG	ENST00000643232.1	n.289-7830C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.739 AC: 112343 AN: 152018 Hom.: 44117 Cov.: 33

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.752

Gnomad AMR AF: 0.788

Gnomad ASJ AF: 0.893

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.879

Gnomad FIN AF: 0.839

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.870

Gnomad OTH AF: 0.775

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

GnomAD4 genome AF: 0.739 AC: 112384 AN: 152136 Hom.: 44126 Cov.: 33 AF XY: 0.742 AC XY: 55160 AN XY: 74386

African (AFR) AF: 0.447 AC: 18510 AN: 41440

American (AMR) AF: 0.788 AC: 12055 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.893 AC: 3102 AN: 3472

East Asian (EAS) AF: 0.741 AC: 3836 AN: 5174

South Asian (SAS) AF: 0.879 AC: 4233 AN: 4816

European-Finnish (FIN) AF: 0.839 AC: 8894 AN: 10604

Middle Eastern (MID) AF: 0.935 AC: 275 AN: 294

European-Non Finnish (NFE) AF: 0.870 AC: 59152 AN: 68022

Other (OTH) AF: 0.778 AC: 1644 AN: 2114

Alfa AF: 0.836 Hom.: 34233

Bravo AF: 0.718

Asia WGS AF: 0.802 AC: 2791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.45
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs1807871; hg19: chr1-55780821;