rs11192851

Variant names:

• chr10-106366562-A-C
• rs11192851

Variant summary

Our verdict is Benign. The variant received -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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.509
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.163 AC: 6774 AN: 41498

American (AMR) AF: 0.344 AC: 5251 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 1047 AN: 3466

East Asian (EAS) AF: 0.152 AC: 785 AN: 5176

South Asian (SAS) AF: 0.320 AC: 1542 AN: 4824

European-Finnish (FIN) AF: 0.335 AC: 3537 AN: 10558

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.394 AC: 26799 AN: 67946

Other (OTH) AF: 0.362 AC: 765 AN: 2112

Alfa AF: 0.318 Hom.: 1560

Bravo AF: 0.300

Asia WGS AF: 0.204 AC: 710 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	9.9
DANN	Benign	0.65
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs11192851; hg19: chr10-108126320;