rs10489489

Positions:

• chr1-55322085-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000643232.1(MIR4422HG):​n.289-893G>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 0.0361 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.491

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=-0.88).
• 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 male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 96 gene

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.289-893G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0463

Gnomad4 AMR AF: 0.0286

Gnomad4 ASJ AF: 0.0251

Gnomad4 EAS AF: 0.0382

Gnomad4 SAS AF: 0.00976

Gnomad4 FIN AF: 0.0273

Gnomad4 NFE AF: 0.0356

Gnomad4 OTH AF: 0.0369

Alfa AF: 0.0368 Hom.: 109

Bravo AF: 0.0372

Asia WGS AF: 0.0180 AC: 63 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10489489; hg19: chr1-55787758;