rs10489489

Variant names:

• chr1-55322085-G-A
• rs10489489
• ENST00000643232.1:n.289-893G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-55322085-G-A
• chr1-55322085-G-C
• chr1-55322085-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000643232.1(MIR4422HG):​n.289-893G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0361 in 152,240 control chromosomes in the GnomAD database, including 96 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 0.036 (96 hom., cov: 32)
• Consequence: MIR4422HG ENST00000643232.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.491
• Publications: 1 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=-0.88).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0361 (5489/152240) while in subpopulation AFR AF = 0.0463 (1924/41536). AF 95% confidence interval is 0.0446. There are 96 homozygotes in GnomAd4. There are 2649 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 96 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000643232.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR4422HG	ENST00000643232.1		n.289-893G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0361 AC: 5486 AN: 152122 Hom.: 96 Cov.: 32

Gnomad AFR AF: 0.0464

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0286

Gnomad ASJ AF: 0.0251

Gnomad EAS AF: 0.0381

Gnomad SAS AF: 0.00954

Gnomad FIN AF: 0.0273

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0356

Gnomad OTH AF: 0.0372

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

GnomAD4 genome AF: 0.0361 AC: 5489 AN: 152240 Hom.: 96 Cov.: 32 AF XY: 0.0356 AC XY: 2649 AN XY: 74430

African (AFR) AF: 0.0463 AC: 1924 AN: 41536

American (AMR) AF: 0.0286 AC: 437 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0251 AC: 87 AN: 3468

East Asian (EAS) AF: 0.0382 AC: 198 AN: 5190

South Asian (SAS) AF: 0.00976 AC: 47 AN: 4816

European-Finnish (FIN) AF: 0.0273 AC: 289 AN: 10598

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0356 AC: 2422 AN: 68010

Other (OTH) AF: 0.0369 AC: 78 AN: 2116

Alfa AF: 0.0368 Hom.: 173

Bravo AF: 0.0372

Asia WGS AF: 0.0180 AC: 63 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.57
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs10489489; hg19: chr1-55787758;