rs11192851

Positions:

• chr10-106366562-A-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 0.309 in 152,048 control chromosomes in the GnomAD database, including 8,104 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 0.31 (8104 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.509

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.106366562A>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46951 AN: 151928 Hom.: 8103 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.309 AC: 46964 AN: 152048 Hom.: 8104 Cov.: 32 AF XY: 0.308 AC XY: 22881 AN XY: 74320

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.344

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.335

Gnomad4 NFE AF: 0.394

Gnomad4 OTH AF: 0.362

Alfa AF: 0.323 Hom.: 1546

Bravo AF: 0.300

Asia WGS AF: 0.204 AC: 710 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	9.9
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11192851; hg19: chr10-108126320;