chr11-122185619-G-T

Variant names:

• chr11-122185619-G-T
• rs6589913
• ENST00000527474.5:n.899-5221C>A

Variant summary

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

The ENST00000527474.5(MIR100HG):​n.899-5221C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 152,050 control chromosomes in the GnomAD database, including 17,709 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 0.48 (17709 hom., cov: 33)
• Consequence: MIR100HG ENST00000527474.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.455
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR100HG	NR_024430.2	n.347-5221C>A		intron_variant	Intron 1 of 3
MIR100HG	NR_137179.1	n.301-5221C>A		intron_variant	Intron 2 of 4
MIR100HG	NR_137180.1	n.359-5221C>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR100HG	ENST00000527474.5	n.899-5221C>A		intron_variant	Intron 3 of 3	1
MIR100HG	ENST00000534782.4	n.325-5221C>A		intron_variant	Intron 1 of 2	1
MIR100HG	ENST00000532350.6	n.325-5221C>A		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72270 AN: 151932 Hom.: 17691 Cov.: 33

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.476 AC: 72320 AN: 152050 Hom.: 17709 Cov.: 33 AF XY: 0.470 AC XY: 34948 AN XY: 74308

African (AFR) AF: 0.423 AC: 17540 AN: 41484

American (AMR) AF: 0.391 AC: 5968 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1734 AN: 3470

East Asian (EAS) AF: 0.225 AC: 1164 AN: 5176

South Asian (SAS) AF: 0.524 AC: 2517 AN: 4804

European-Finnish (FIN) AF: 0.480 AC: 5057 AN: 10544

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.542 AC: 36855 AN: 67988

Other (OTH) AF: 0.465 AC: 982 AN: 2110

Alfa AF: 0.511 Hom.: 63255

Bravo AF: 0.460

Asia WGS AF: 0.340 AC: 1188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.18
DANN	Benign	0.19
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs6589913; hg19: chr11-122056327;