rs17126243

Variant names:

• chr11-122178967-G-A
• rs17126243
• ENST00000534782.4:n.387+1369C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-122178967-G-A
• chr11-122178967-G-C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 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=-0.89).
• 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 rank	MANE	Protein	UniProt
MIR100HG	NR_024430.2	n.409+1369C>T		intron_variant	Intron 2 of 3
MIR100HG	NR_137179.1	n.363+1369C>T		intron_variant	Intron 3 of 4
MIR100HG	NR_137180.1	n.421+1369C>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR100HG	ENST00000534782.4	n.387+1369C>T		intron_variant	Intron 2 of 2	1
MIR100HG	ENST00000532350.6	n.387+1369C>T		intron_variant	Intron 2 of 2	5
MIR100HG	ENST00000533109.6	n.916+1369C>T		intron_variant	Intron 6 of 6	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

African (AFR) AF: 0.141 AC: 5831 AN: 41500

American (AMR) AF: 0.108 AC: 1649 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0222 AC: 77 AN: 3470

East Asian (EAS) AF: 0.0104 AC: 54 AN: 5176

South Asian (SAS) AF: 0.0373 AC: 180 AN: 4820

European-Finnish (FIN) AF: 0.0698 AC: 740 AN: 10606

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0602 AC: 4095 AN: 68002

Other (OTH) AF: 0.0729 AC: 154 AN: 2112

Alfa AF: 0.0623 Hom.: 596

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
PhyloP100		-1.6
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

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