11-122178967-G-A

Position:

• chr11-122178967-G-A

Variant summary

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

The ENST00000534782.4(MIR100HG):​n.387+1369C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0851 in 152,164 control chromosomes in the GnomAD database, including 664 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 (664 hom., cov: 32)
• Consequence: MIR100HG ENST00000534782.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58

Genes affected

MIR100HG (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR100HG	NR_024430.2	n.409+1369C>T		intron_variant
MIR100HG	NR_137179.1	n.363+1369C>T		intron_variant
MIR100HG	NR_137180.1	n.421+1369C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR100HG	ENST00000534782.4	n.387+1369C>T		intron_variant		1
MIR100HG	ENST00000532350.6	n.387+1369C>T		intron_variant		5
MIR100HG	ENST00000533109.6	n.916+1369C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.0851 AC: 12936 AN: 152046 Hom.: 664 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.0222

Gnomad EAS AF: 0.0104

Gnomad SAS AF: 0.0373

Gnomad FIN AF: 0.0698

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0602

Gnomad OTH AF: 0.0742

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

GnomAD4 genome AF: 0.0851 AC: 12954 AN: 152164 Hom.: 664 Cov.: 32 AF XY: 0.0848 AC XY: 6309 AN XY: 74380

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.0222

Gnomad4 EAS AF: 0.0104

Gnomad4 SAS AF: 0.0373

Gnomad4 FIN AF: 0.0698

Gnomad4 NFE AF: 0.0602

Gnomad4 OTH AF: 0.0729

Alfa AF: 0.0574 Hom.: 349

Bravo AF: 0.0897

Asia WGS AF: 0.0360 AC: 126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.66
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17126243; hg19: chr11-122049675; COSMIC: COSV73190213;