rs605335

Variant names:

• chr11-82201688-A-G
• rs605335
• ENST00000500502.5:n.432-101481T>C

Variant summary

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

The ENST00000500502.5(MIR4300HG):​n.432-101481T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 151,900 control chromosomes in the GnomAD database, including 10,424 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 0.36 (10424 hom., cov: 31)
• Consequence: MIR4300HG ENST00000500502.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190
• Publications: 0 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR4300HG	NR_120571.1	n.432-101481T>C		intron_variant	Intron 3 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR4300HG	ENST00000500502.5	n.432-101481T>C		intron_variant	Intron 3 of 7	1
MIR4300HG	ENST00000532217.1	n.558-101481T>C		intron_variant	Intron 4 of 4	5
MIR4300HG	ENST00000653173.1	n.185-101481T>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54694 AN: 151782 Hom.: 10401 Cov.: 31

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.361 AC: 54772 AN: 151900 Hom.: 10424 Cov.: 31 AF XY: 0.362 AC XY: 26869 AN XY: 74232

African (AFR) AF: 0.463 AC: 19156 AN: 41418

American (AMR) AF: 0.406 AC: 6198 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1409 AN: 3464

East Asian (EAS) AF: 0.486 AC: 2508 AN: 5158

South Asian (SAS) AF: 0.313 AC: 1507 AN: 4810

European-Finnish (FIN) AF: 0.271 AC: 2843 AN: 10502

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20091 AN: 67944

Other (OTH) AF: 0.356 AC: 753 AN: 2114

Alfa AF: 0.333 Hom.: 1151

Bravo AF: 0.376

Asia WGS AF: 0.382 AC: 1326 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.7
DANN	Benign	0.80
PhyloP100		0.019

Splicing

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

Other links and lift over

dbSNP: rs605335; hg19: chr11-81912730;