rs1945906

Variant names:

• chr11-81850035-A-C
• rs1945906
• ENST00000653173.1:n.419-25104T>G

Variant summary

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

The ENST00000653173.1(MIR4300HG):​n.419-25104T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 151,458 control chromosomes in the GnomAD database, including 8,178 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 0.32 (8178 hom., cov: 31)
• Consequence: MIR4300HG ENST00000653173.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.36
• Publications: 5 publications found

Genes affected

MIR4300HG (HGNC:52003): (MIR4300 host gene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000653173.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR4300HG	ENST00000653173.1		n.419-25104T>G		intron	N/A
	MIR4300HG	ENST00000659248.1		n.666-25104T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48592 AN: 151342 Hom.: 8167 Cov.: 31

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.321 AC: 48629 AN: 151458 Hom.: 8178 Cov.: 31 AF XY: 0.330 AC XY: 24413 AN XY: 73994

African (AFR) AF: 0.261 AC: 10810 AN: 41398

American (AMR) AF: 0.395 AC: 5979 AN: 15154

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1254 AN: 3458

East Asian (EAS) AF: 0.590 AC: 3041 AN: 5156

South Asian (SAS) AF: 0.257 AC: 1237 AN: 4816

European-Finnish (FIN) AF: 0.441 AC: 4653 AN: 10544

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.303 AC: 20491 AN: 67626

Other (OTH) AF: 0.349 AC: 732 AN: 2100

Alfa AF: 0.307 Hom.: 3809

Bravo AF: 0.321

Asia WGS AF: 0.382 AC: 1326 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	7.7
DANN	Benign	0.79
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs1945906; hg19: chr11-81561077;