11-122177617-C-T

Variant names:

• chr11-122177617-C-T
• rs676943
• ENST00000534782.4:n.387+2719G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000534782.4(MIR100HG):​n.387+2719G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.534 in 151,938 control chromosomes in the GnomAD database, including 22,265 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 (22265 hom., cov: 32)
• Consequence: MIR100HG ENST00000534782.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0560
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000534782.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR100HG	NR_024430.2		n.409+2719G>A		intron	N/A
	MIR100HG	NR_137179.1		n.363+2719G>A		intron	N/A
	MIR100HG	NR_137180.1		n.421+2719G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR100HG	ENST00000534782.4	TSL:1	n.387+2719G>A		intron	N/A
	MIR100HG	ENST00000532350.6	TSL:5	n.387+2719G>A		intron	N/A
	MIR100HG	ENST00000533109.6	TSL:5	n.916+2719G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.534 AC: 81025 AN: 151820 Hom.: 22224 Cov.: 32

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.534 AC: 81112 AN: 151938 Hom.: 22265 Cov.: 32 AF XY: 0.535 AC XY: 39700 AN XY: 74242

African (AFR) AF: 0.662 AC: 27456 AN: 41448

American (AMR) AF: 0.587 AC: 8962 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1725 AN: 3470

East Asian (EAS) AF: 0.603 AC: 3096 AN: 5138

South Asian (SAS) AF: 0.470 AC: 2260 AN: 4810

European-Finnish (FIN) AF: 0.474 AC: 5007 AN: 10558

Middle Eastern (MID) AF: 0.462 AC: 135 AN: 292

European-Non Finnish (NFE) AF: 0.453 AC: 30759 AN: 67948

Other (OTH) AF: 0.545 AC: 1148 AN: 2106

Alfa AF: 0.304 Hom.: 672

Bravo AF: 0.555

Asia WGS AF: 0.595 AC: 2065 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.7
DANN	Benign	0.71
PhyloP100		0.056

Splicing

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

Other links and lift over

dbSNP: rs676943; hg19: chr11-122048325;