rs674916

chr11-82265825-G-A

Variant summary

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

The NR_120571.1(MIR4300HG):n.431+84101C>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 0.0894 in 152,040 control chromosomes in the GnomAD database, including 652 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 0.089 (652 hom., cov: 32)
• Consequence: MIR4300HG NR_120571.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.432

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 (AMR) allele frequency at 95% confidence interval = 0.103 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR4300HG	NR_120571.1	n.431+84101C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR4300HG	ENST00000532217.1	n.557+90687C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0893 AC: 13569 AN: 151922 Hom.: 648 Cov.: 32

Gnomad AFR AF: 0.0796

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0995

Gnomad EAS AF: 0.00290

Gnomad SAS AF: 0.0399

Gnomad FIN AF: 0.0568

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.0894 AC: 13588 AN: 152040 Hom.: 652 Cov.: 32 AF XY: 0.0878 AC XY: 6526 AN XY: 74340

Gnomad4 AFR AF: 0.0796

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.0995

Gnomad4 EAS AF: 0.00290

Gnomad4 SAS AF: 0.0395

Gnomad4 FIN AF: 0.0568

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.104

Alfa AF: 0.0990 Hom.: 101

Bravo AF: 0.0932

Asia WGS AF: 0.0300 AC: 106 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.71
Dann	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs674916; hg19: chr11-81976867;