rs17111925

Variant names:

• chr1-55323678-G-A
• rs17111925
• ENST00000643232.1:n.989G>A

Variant summary

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

The ENST00000643232.1(MIR4422HG):​n.989G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0448 in 153,924 control chromosomes in the GnomAD database, including 216 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 0.045 (214 hom., cov: 33)
  • Exomes 𝑓: 0.046 (2 hom.)
• Consequence: MIR4422HG ENST00000643232.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.678
• Publications: 2 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.115 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.989G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0448 AC: 6814 AN: 152184 Hom.: 215 Cov.: 33

Gnomad AFR AF: 0.0104

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0400

Gnomad ASJ AF: 0.0349

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.0582

Gnomad FIN AF: 0.0503

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0598

Gnomad OTH AF: 0.0522

GnomAD4 exome AF: 0.0462 AC: 75 AN: 1622 Hom.: 2 Cov.: 0 AF XY: 0.0471 AC XY: 44 AN XY: 934

African (AFR) AF: 0.00 AC: 0 AN: 22

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.132 AC: 10 AN: 76

South Asian (SAS) AF: 0.0652 AC: 3 AN: 46

European-Finnish (FIN) AF: 0.0372 AC: 16 AN: 430

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 8

European-Non Finnish (NFE) AF: 0.0445 AC: 40 AN: 898

Other (OTH) AF: 0.0429 AC: 6 AN: 140

GnomAD4 genome AF: 0.0447 AC: 6814 AN: 152302 Hom.: 214 Cov.: 33 AF XY: 0.0451 AC XY: 3362 AN XY: 74468

African (AFR) AF: 0.0104 AC: 431 AN: 41562

American (AMR) AF: 0.0400 AC: 612 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0349 AC: 121 AN: 3470

East Asian (EAS) AF: 0.123 AC: 639 AN: 5182

South Asian (SAS) AF: 0.0590 AC: 285 AN: 4828

European-Finnish (FIN) AF: 0.0503 AC: 534 AN: 10612

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0598 AC: 4068 AN: 68024

Other (OTH) AF: 0.0517 AC: 109 AN: 2110

Alfa AF: 0.0506 Hom.: 183

Bravo AF: 0.0429

Asia WGS AF: 0.0850 AC: 296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.6
DANN	Benign	0.75
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs17111925; hg19: chr1-55789351;