rs565229

Positions:

• chr11-122318757-G-A
• chr11-122318757-G-T

Variant summary

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

The ENST00000527474.5(MIR100HG):​n.479-25151C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,072 control chromosomes in the GnomAD database, including 1,195 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 0.12 (1195 hom., cov: 32)
• Consequence: MIR100HG ENST00000527474.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.657

Genes affected

MIR100HG (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR100HG	NR_137179.1	n.181-26354C>T		intron_variant
MIR100HG	NR_137192.1	n.494-26354C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR100HG	ENST00000527474.5	n.479-25151C>T		intron_variant		1
MIR100HG	ENST00000526674.1	n.181-26354C>T		intron_variant		5
MIR100HG	ENST00000528381.1	n.321-26354C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18147 AN: 151952 Hom.: 1195 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.0994

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.119 AC: 18167 AN: 152072 Hom.: 1195 Cov.: 32 AF XY: 0.122 AC XY: 9079 AN XY: 74332

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.266

Gnomad4 SAS AF: 0.0993

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.113

Alfa AF: 0.112 Hom.: 1340

Bravo AF: 0.118

Asia WGS AF: 0.182 AC: 633 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.9
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs565229; hg19: chr11-122189465;