rs11198446

Variant names:

• chr10-118482700-C-T
• rs11198446

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 0.0716 in 152,142 control chromosomes in the GnomAD database, including 753 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 0.072 (753 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.501
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0714 AC: 10849 AN: 152024 Hom.: 749 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.0377

Gnomad ASJ AF: 0.0580

Gnomad EAS AF: 0.0439

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.0105

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0236

Gnomad OTH AF: 0.0621

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

GnomAD4 genome AF: 0.0716 AC: 10887 AN: 152142 Hom.: 753 Cov.: 32 AF XY: 0.0715 AC XY: 5318 AN XY: 74378

African (AFR) AF: 0.179 AC: 7444 AN: 41480

American (AMR) AF: 0.0377 AC: 576 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0580 AC: 201 AN: 3468

East Asian (EAS) AF: 0.0442 AC: 229 AN: 5186

South Asian (SAS) AF: 0.109 AC: 522 AN: 4810

European-Finnish (FIN) AF: 0.0105 AC: 111 AN: 10584

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0236 AC: 1608 AN: 68006

Other (OTH) AF: 0.0615 AC: 130 AN: 2114

Alfa AF: 0.0376 Hom.: 407

Bravo AF: 0.0765

Asia WGS AF: 0.0990 AC: 346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.62
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs11198446; hg19: chr10-120242212;