rs531897

Positions:

• chr11-122142461-C-T

Variant summary

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

The ENST00000534782.4(MIR100HG):​n.387+37875G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.669 in 152,148 control chromosomes in the GnomAD database, including 34,203 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 0.67 (34203 hom., cov: 33)
• Consequence: MIR100HG ENST00000534782.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.445

Genes affected

MIR100HG (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR100HG	NR_024430.2	n.491+13090G>A		intron_variant
MIR100HG	NR_137179.1	n.445+13090G>A		intron_variant
MIR100HG	NR_137180.1	n.503+13090G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR100HG	ENST00000534782.4	n.387+37875G>A		intron_variant		1
MIR100HG	ENST00000534297.2	n.185+13090G>A		intron_variant		4
MIR100HG	ENST00000637700.1	n.681+13090G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.669 AC: 101665 AN: 152030 Hom.: 34169 Cov.: 33

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.653

Gnomad EAS AF: 0.652

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.669 AC: 101751 AN: 152148 Hom.: 34203 Cov.: 33 AF XY: 0.670 AC XY: 49854 AN XY: 74386

Gnomad4 AFR AF: 0.634

Gnomad4 AMR AF: 0.717

Gnomad4 ASJ AF: 0.653

Gnomad4 EAS AF: 0.653

Gnomad4 SAS AF: 0.495

Gnomad4 FIN AF: 0.760

Gnomad4 NFE AF: 0.678

Gnomad4 OTH AF: 0.673

Alfa AF: 0.677 Hom.: 58673

Bravo AF: 0.669

Asia WGS AF: 0.590 AC: 2051 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs531897; hg19: chr11-122013169;