11-81871697-T-C

Position:

• chr11-81871697-T-C

Variant summary

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

The ENST00000653173.1(MIR4300HG):​n.419-46766A>G 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 0.774 in 151,678 control chromosomes in the GnomAD database, including 46,179 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 0.77 (46179 hom., cov: 31)
• Consequence: MIR4300HG ENST00000653173.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.909 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR4300HG	ENST00000653173.1	n.419-46766A>G		intron_variant, non_coding_transcript_variant
MIR4300HG	ENST00000659248.1	n.666-46766A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.774 AC: 117291 AN: 151562 Hom.: 46131 Cov.: 31

Gnomad AFR AF: 0.917

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.674

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.801

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.743

Gnomad OTH AF: 0.750

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

GnomAD4 genome AF: 0.774 AC: 117398 AN: 151678 Hom.: 46179 Cov.: 31 AF XY: 0.769 AC XY: 57004 AN XY: 74086

Gnomad4 AFR AF: 0.917

Gnomad4 AMR AF: 0.705

Gnomad4 ASJ AF: 0.674

Gnomad4 EAS AF: 0.531

Gnomad4 SAS AF: 0.800

Gnomad4 FIN AF: 0.667

Gnomad4 NFE AF: 0.743

Gnomad4 OTH AF: 0.750

Alfa AF: 0.752 Hom.: 10598

Bravo AF: 0.775

Asia WGS AF: 0.719 AC: 2501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.32
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1459952; hg19: chr11-81582739;