rs11198446

Variant names:

• chr10-118482700-C-T
• rs11198446

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 0.0716 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

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 (AFR) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.0377

Gnomad4 ASJ AF: 0.0580

Gnomad4 EAS AF: 0.0442

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.0105

Gnomad4 NFE AF: 0.0236

Gnomad4 OTH AF: 0.0615

Alfa AF: 0.0339 Hom.: 217

Bravo AF: 0.0765

Asia WGS AF: 0.0990 AC: 346 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	1.1
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11198446; hg19: chr10-120242212;