rs2084637

Positions:

• chr11-122520479-T-C

Variant summary

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

The variant allele was found at a frequency of 0.274 in 152,116 control chromosomes in the GnomAD database, including 6,659 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 0.27 (6659 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.108

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.122520479T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR100HG	ENST00000533109.6	n.433+19000A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41668 AN: 151998 Hom.: 6667 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.383

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.274 AC: 41656 AN: 152116 Hom.: 6659 Cov.: 32 AF XY: 0.275 AC XY: 20460 AN XY: 74336

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.296

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.387

Gnomad4 NFE AF: 0.353

Gnomad4 OTH AF: 0.270

Alfa AF: 0.334 Hom.: 17476

Bravo AF: 0.251

Asia WGS AF: 0.352 AC: 1224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	7.8
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2084637; hg19: chr11-122391187;