rs657514

Positions:

• chr11-122174496-C-A

Variant summary

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

The ENST00000654571.2(MIR100HG):​n.1470G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.532 in 151,824 control chromosomes in the GnomAD database, including 21,547 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 (21547 hom., cov: 32)
• Consequence: MIR100HG ENST00000654571.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.393

Genes affected

MIR100HG (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR100HG	NR_024430.2	n.409+5840G>T		intron_variant
MIR100HG	NR_137179.1	n.363+5840G>T		intron_variant
MIR100HG	NR_137180.1	n.421+5840G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR100HG	ENST00000534782.4	n.387+5840G>T		intron_variant		1
MIR100HG	ENST00000654571.2	n.1470G>T		non_coding_transcript_exon_variant	5/5
MIR100HG	ENST00000660329.2	n.855G>T		non_coding_transcript_exon_variant	5/5

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80719 AN: 151706 Hom.: 21525 Cov.: 32

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.532 AC: 80778 AN: 151824 Hom.: 21547 Cov.: 32 AF XY: 0.533 AC XY: 39570 AN XY: 74180

Gnomad4 AFR AF: 0.578

Gnomad4 AMR AF: 0.536

Gnomad4 ASJ AF: 0.541

Gnomad4 EAS AF: 0.581

Gnomad4 SAS AF: 0.474

Gnomad4 FIN AF: 0.536

Gnomad4 NFE AF: 0.502

Gnomad4 OTH AF: 0.543

Alfa AF: 0.509 Hom.: 3574

Bravo AF: 0.539

Asia WGS AF: 0.580 AC: 2013 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.7
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs657514; hg19: chr11-122045204;