rs657514

Positions:

• chr11-122174496-C-A

Variant summary

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

The ENST00000533109.6(MIR100HG):​n.916+5840G>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 0.532 in 151,824 control chromosomes in the GnomAD database, including 21,547 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 0.53 (21547 hom., cov: 32)
• Consequence: MIR100HG ENST00000533109.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.393

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR100HG	NR_024430.2	n.409+5840G>T		intron_variant, non_coding_transcript_variant
MIR100HG	NR_137179.1	n.363+5840G>T		intron_variant, non_coding_transcript_variant
MIR100HG	NR_137180.1	n.421+5840G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR100HG	ENST00000533109.6	n.916+5840G>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80719 AN: 151706 Hom.: 21525 Cov.: 32

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.532 AC: 80778 AN: 151824 Hom.: 21547 Cov.: 32 AF XY: 0.533 AC XY: 39570 AN XY: 74180

Gnomad4 AFR AF: 0.578

Gnomad4 AMR AF: 0.536

Gnomad4 ASJ AF: 0.541

Gnomad4 EAS AF: 0.581

Gnomad4 SAS AF: 0.474

Gnomad4 FIN AF: 0.536

Gnomad4 NFE AF: 0.502

Gnomad4 OTH AF: 0.543

Alfa AF: 0.509 Hom.: 3574

Bravo AF: 0.539

Asia WGS AF: 0.580 AC: 2013 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.7
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs657514; hg19: chr11-122045204;