rs678021

chr11-82043646-C-T

Variant summary

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

The NR_120571.1(MIR4300HG):n.814-27912G>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 0.0846 in 152,208 control chromosomes in the GnomAD database, including 689 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 0.085 (689 hom., cov: 32)
• Consequence: MIR4300HG NR_120571.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.11

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) 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.814-27912G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR4300HG	ENST00000500502.5	n.814-27912G>A		intron_variant, non_coding_transcript_variant		1
MIR4300HG	ENST00000530896.6	n.346-27912G>A		intron_variant, non_coding_transcript_variant		3
MIR4300HG	ENST00000653173.1	n.418+56328G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0845 AC: 12857 AN: 152090 Hom.: 684 Cov.: 32

Gnomad AFR AF: 0.0297

Gnomad AMI AF: 0.131

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.0884

Gnomad EAS AF: 0.00385

Gnomad SAS AF: 0.0509

Gnomad FIN AF: 0.0758

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.0846 AC: 12876 AN: 152208 Hom.: 689 Cov.: 32 AF XY: 0.0831 AC XY: 6185 AN XY: 74422

Gnomad4 AFR AF: 0.0296

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.0884

Gnomad4 EAS AF: 0.00386

Gnomad4 SAS AF: 0.0514

Gnomad4 FIN AF: 0.0758

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.106

Alfa AF: 0.106 Hom.: 154

Bravo AF: 0.0906

Asia WGS AF: 0.0380 AC: 133 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	0.083
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs678021; hg19: chr11-81754688;