rs10840491

Positions:

• chr11-2173160-G-A

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 0.144 in 154,202 control chromosomes in the GnomAD database, including 1,655 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 0.14 (1630 hom., cov: 33)
  • Exomes 𝑓: 0.14 (25 hom.)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.574

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.2173160G>A		intergenic_region
MIR4686	NR_039834.1	n.*22G>A		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR4686	ENST00000584128.1	n.*22G>A		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21926 AN: 151936 Hom.: 1626 Cov.: 33

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.140

GnomAD3 exomes AF: 0.113 AC: 45 AN: 400 Hom.: 2 AF XY: 0.110 AC XY: 24 AN XY: 218

Gnomad AFR exome AF: 0.250

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.114

Gnomad OTH exome AF: 0.0833

GnomAD4 exome AF: 0.136 AC: 292 AN: 2148 Hom.: 25 Cov.: 0 AF XY: 0.134 AC XY: 144 AN XY: 1074

Gnomad4 AFR exome AF: 0.122

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.178

Gnomad4 FIN exome AF: 0.300

Gnomad4 NFE exome AF: 0.141

Gnomad4 OTH exome AF: 0.0966

GnomAD4 genome AF: 0.144 AC: 21948 AN: 152054 Hom.: 1630 Cov.: 33 AF XY: 0.146 AC XY: 10865 AN XY: 74338

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.171

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.142

Alfa AF: 0.140 Hom.: 1310

Bravo AF: 0.148

Asia WGS AF: 0.146 AC: 508 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	6.8
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10840491; hg19: chr11-2194390;