rs629367

chr11-122146306-C-Achr11-122146306-C-Gchr11-122146306-C-T

Variant summary

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

The ENST00000534782.4(MIR100HG):n.387+34030G>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 0.874 in 152,176 control chromosomes in the GnomAD database, including 58,183 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 0.87 (58183 hom., cov: 32)
• Consequence: MIR100HG ENST00000534782.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.324

Genes affected

MIR100HG (HGNC:39522): (mir-100-let-7a-2-mir-125b-1 cluster host gene) This gene produces long non-coding RNAs that act as regulators of cell proliferation. Alternative promoter usage and splicing results in multiple transcript variants. Some transcript variants may promote growth, while others may act to negatively regulate cell division. [provided by RefSeq, May 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR100HG	NR_024430.2	n.491+9245G>T		intron_variant, non_coding_transcript_variant
MIR100HG	NR_137179.1	n.445+9245G>T		intron_variant, non_coding_transcript_variant
MIR100HG	NR_137180.1	n.503+9245G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR100HG	ENST00000534782.4	n.387+34030G>T		intron_variant, non_coding_transcript_variant		1
MIR100HG	ENST00000534297.2	n.185+9245G>T		intron_variant, non_coding_transcript_variant		4
MIR100HG	ENST00000637700.1	n.681+9245G>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.873 AC: 132806 AN: 152058 Hom.: 58123 Cov.: 32

Gnomad AFR AF: 0.923

Gnomad AMI AF: 0.898

Gnomad AMR AF: 0.870

Gnomad ASJ AF: 0.886

Gnomad EAS AF: 0.766

Gnomad SAS AF: 0.820

Gnomad FIN AF: 0.858

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.858

Gnomad OTH AF: 0.869

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

GnomAD4 genome AF: 0.874 AC: 132932 AN: 152176 Hom.: 58183 Cov.: 32 AF XY: 0.871 AC XY: 64841 AN XY: 74406

Gnomad4 AFR AF: 0.923

Gnomad4 AMR AF: 0.870

Gnomad4 ASJ AF: 0.886

Gnomad4 EAS AF: 0.767

Gnomad4 SAS AF: 0.821

Gnomad4 FIN AF: 0.858

Gnomad4 NFE AF: 0.858

Gnomad4 OTH AF: 0.871

Alfa AF: 0.873 Hom.: 10749

Bravo AF: 0.876

Asia WGS AF: 0.803 AC: 2790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	2.6
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs629367; hg19: chr11-122017014; COSMIC: COSV62996667;