11-122083949-G-A

Position:

• chr11-122083949-G-A

Variant summary

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

The NR_137178.1(MIR100HG):​n.473+16425C>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 0.262 in 151,968 control chromosomes in the GnomAD database, including 5,786 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 0.26 (5786 hom., cov: 31)
• Consequence: MIR100HG NR_137178.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.234

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR100HG	NR_137178.1	n.473+16425C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR100HG	ENST00000530955.2	n.256+17498C>T		intron_variant, non_coding_transcript_variant		5
MIR100HG	ENST00000532319.2	n.119+16425C>T		intron_variant, non_coding_transcript_variant		4
MIR100HG	ENST00000636654.1	n.75+16425C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39698 AN: 151850 Hom.: 5768 Cov.: 31

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.0516

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.220

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.262 AC: 39766 AN: 151968 Hom.: 5786 Cov.: 31 AF XY: 0.257 AC XY: 19094 AN XY: 74272

Gnomad4 AFR AF: 0.390

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.0514

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.208

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.273

Alfa AF: 0.229 Hom.: 8464

Bravo AF: 0.267

Asia WGS AF: 0.172 AC: 598 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	0.29
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7121446; hg19: chr11-121954657;