chr11-81905181-C-A

Position:

• chr11-81905181-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_120571.1(MIR4300HG):​n.941-22885G>T 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 0.0708 in 152,032 control chromosomes in the GnomAD database, including 562 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 0.071 (562 hom., cov: 32)
• Consequence: MIR4300HG NR_120571.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.620

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR4300HG	NR_120571.1	n.941-22885G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR4300HG	ENST00000500502.5	n.941-22885G>T		intron_variant, non_coding_transcript_variant		1
MIR4300HG	ENST00000530896.6	n.473-22885G>T		intron_variant, non_coding_transcript_variant		3
MIR4300HG	ENST00000653173.1	n.419-80250G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0706 AC: 10728 AN: 151914 Hom.: 557 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.0544

Gnomad ASJ AF: 0.0542

Gnomad EAS AF: 0.000580

Gnomad SAS AF: 0.0209

Gnomad FIN AF: 0.0207

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0468

Gnomad OTH AF: 0.0627

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

GnomAD4 genome AF: 0.0708 AC: 10759 AN: 152032 Hom.: 562 Cov.: 32 AF XY: 0.0679 AC XY: 5050 AN XY: 74344

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.0543

Gnomad4 ASJ AF: 0.0542

Gnomad4 EAS AF: 0.000581

Gnomad4 SAS AF: 0.0205

Gnomad4 FIN AF: 0.0207

Gnomad4 NFE AF: 0.0468

Gnomad4 OTH AF: 0.0625

Alfa AF: 0.0580 Hom.: 58

Bravo AF: 0.0769

Asia WGS AF: 0.0240 AC: 83 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.27
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7944477; hg19: chr11-81616223;